galaxy-dev October 2011

galaxy-dev@lists.galaxyproject.org

90 participants
149 discussions

broken-pipe error on NGS Fastq tools "clip"
by Colleen Doherty 05 Oct '11

05 Oct '11

I am trying to set up a local instance. When running Clip adapter sequences I get the following error: fastx_clipper: Invalid quality score value (char 'J' ord 74 quality value 41) on line 36 gzip: stdout: Broken pipe I'm stuck on where to try to trouble-shoot this. This is on groomed fastq data in my history. I have the same error on other datasets. Other tools (Bowtie, FastQC) work on this dataset. I'm confused why it is gzip (but I clearly don't understand how Galaxy stores the data). Thanks for any suggestions!

2 2

prevent downloaded files with .txt added
by David Hoover 05 Oct '11

05 Oct '11

Does anyone know how to prevent the .txt suffix from being added to files downloaded from Galaxy? For example, a fasta file is downloaded as xxx.fasta.txt, instead of xxx.fasta. Wondering, David Hoover Helix Systems Staff http://helix.nih.gov

2 2

Restarting Galaxy-cloud gives: cloud instance missing /opt/sge/default/common directory
by Colleen Doherty 04 Oct '11

04 Oct '11

Hello, When I stop and restart an instance of galaxy I am not able to bring it back up. I believe I have the exact same error described here: http://gmod.827538.n3.nabble.com/cloud-instance-missing-opt-sge-default-com… Basically I do not have the following files, therefore sge won't start up, so no galaxy. -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory 1. Is it just not advisable to stop and restart? Should I just start a fresh instance every time? (Is that any difference in cost?) 2. If stopping and restarting are OK- Are there things I should do before shutting down that would prevent this? I did find sge.py from galaxy cloudman (which looks like something I should have done) 3. If I need to start a new instance, will someone provide an example of the line for userdata that allows me to link to my current bucket? Thanks for any advice (and apologies if this should be in galaxy-users). output from /mnt/cm/paster.log is below- but I did try to mess around with this a bit (restarting, shutting things down before copying this, so it may not be very diagnostic, sorry). Thank you, Colleen [ERROR] misc:514 2011-10-03 20:55:37,222: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 20:55:37,223: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 20:55:37,223: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 20:55:38,059: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 20:55:39,657: Configuring SGE... [DEBUG] sge:104 2011-10-03 20:55:39,658: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 20:55:39,659: Setting up SGE. [ERROR] misc:514 2011-10-03 20:55:39,769: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] galaxy:139 2011-10-03 20:55:47,615: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:55:47,616: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:04,183: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:04,184: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:20,481: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:20,481: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:36,769: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:36,770: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:53,039: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:53,039: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:09,346: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:09,346: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:25,641: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:25,642: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:41,944: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:41,944: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:58,246: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:58,247: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:14,523: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:14,523: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:30,819: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:30,820: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:47,089: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:47,089: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:03,385: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:03,386: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:19,713: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:19,713: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:35,996: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:35,996: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:52,264: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:52,265: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:08,545: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:08,545: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:24,824: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:24,825: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:41,116: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:41,117: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:57,398: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:57,398: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:13,676: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:13,677: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:29,993: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:29,994: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:46,312: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:46,313: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:02,642: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:02,643: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:18,934: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:18,934: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [INFO] sge:28 2011-10-03 21:02:19,073: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:19,079: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 21:02:19,080: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:02:19,080: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:02:19,779: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:02:[ERROR] misc:514 2011-10-03 20:55:37,222: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 20:55:37,223: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 20:55:37,223: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 20:55:38,059: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 20:55:39,657: Configuring SGE... [DEBUG] sge:104 2011-10-03 20:55:39,658: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 20:55:39,659: Setting up SGE. [ERROR] misc:514 2011-10-03 20:55:39,769: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] galaxy:139 2011-10-03 20:55:47,615: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:55:47,616: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:04,183: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:04,184: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:20,481: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:20,481: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:36,769: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:36,770: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:53,039: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:53,039: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:09,346: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:09,346: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:25,641: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:25,642: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:41,944: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:41,944: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:58,246: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:58,247: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:14,523: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:14,523: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:30,819: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:30,820: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:47,089: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:47,089: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:03,385: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:03,386: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:19,713: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:19,713: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:35,996: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:35,996: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:52,264: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:52,265: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:08,545: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:08,545: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:24,824: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:24,825: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:41,116: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:41,117: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:57,398: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:57,398: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:13,676: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:13,677: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:29,993: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:29,994: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:46,312: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:46,313: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:02,642: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:02,643: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:18,934: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:18,934: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [INFO] sge:28 2011-10-03 21:02:19,073: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:19,079: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 21:02:19,080: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:02:19,080: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:02:19,779: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:02:21,313: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:02:21,314: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:02:21,314: Setting up SGE. [ERROR] misc:514 2011-10-03 21:02:21,424: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] root:354 2011-10-03 21:02:30,686: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:02:30,687: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:30,692: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [INFO] sge:28 2011-10-03 21:02:31,978: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:31,983: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 21:02:31,984: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:02:31,984: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:02:32,216: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:02:33,718: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:02:33,719: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:02:33,719: Setting up SGE. [ERROR] misc:514 2011-10-03 21:02:33,830: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] galaxy:139 2011-10-03 21:02:35,204: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:35,205: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:51,478: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:51,478: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:07,771: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:07,772: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:24,109: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:24,109: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:40,384: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:40,384: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:56,651: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:56,651: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:12,920: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:12,921: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:29,215: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:29,215: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:45,524: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:45,524: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:01,832: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:01,832: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:18,100: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:18,101: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:34,374: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:34,374: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:50,636: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:50,637: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:06,984: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:06,985: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:23,253: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:23,254: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:39,536: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:39,537: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:55,787: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:55,788: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] root:354 2011-10-03 21:07:09,086: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:07:09,086: Removing SGE service [ERROR] misc:514 2011-10-03 21:07:09,092: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] root:354 2011-10-03 21:07:10,053: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:07:10,053: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:07:10,053: Shutting down Galaxy... [DEBUG] misc:511 2011-10-03 21:07:11,409: Successfully stopped Galaxy. [DEBUG] master:1510 2011-10-03 21:07:12,062: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Shut down; [DEBUG] root:354 2011-10-03 21:07:13,247: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:07:13,247: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:07:13,247: Shutting down Galaxy... [ERROR] misc:514 2011-10-03 21:07:13,594: Error stopping Galaxy, running command '/bin/su - galaxy -c "sh $GALAXY_HOME/run.sh --stop-daemon"' returned code '1' and following stderr: '' [DEBUG] root:354 2011-10-03 21:07:19,796: Managing services: [<cm.services.apps.postgres.PostgresService object at 0x2af8290>] [INFO] postgres:24 2011-10-03 21:07:19,797: Removing 'Postgres' service [DEBUG] misc:511 2011-10-03 21:07:19,863: Successfully set ownership of Postgres data directory [INFO] postgres:102 2011-10-03 21:07:19,864: Stopping PostgreSQL... [DEBUG] misc:511 2011-10-03 21:07:20,910: Successfully stopped PostgreSQL [DEBUG] root:354 2011-10-03 21:07:25,447: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [DEBUG] sge:61 2011-10-03 21:07:25,447: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:07:25,448: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:07:25,617: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:07:27,074: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:07:27,075: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:07:27,075: Setting up SGE. [ERROR] misc:514 2011-10-03 21:07:27,186: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] master:1510 2011-10-03 21:07:28,269: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:07:44,467: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:00,668: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:16,861: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:33,066: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] root:354 2011-10-03 21:08:44,630: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:08:44,631: Removing SGE service [ERROR] misc:514 2011-10-03 21:08:44,636: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] master:1510 2011-10-03 21:08:49,320: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:05,516: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:21,725: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:37,940: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:54,203: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:10,422: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:26,625: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:42,830: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:59,055: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:15,257: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:31,577: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:47,765: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:03,974: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:20,166: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:36,399: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:52,608: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:08,812: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:25,006: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:41,208: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:57,398: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:13,734: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:29,943: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:46,152: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:02,378: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:18,599: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:34,849: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:51,043: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:07,329: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:23,517: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:39,712: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:56,062: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:17:12,268: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:17:28,489: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] root:354 2011-10-03 21:17:36,296: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:17:36,296: Removing SGE service [ERROR] misc:514 2011-10-03 21:17:36,302: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] root:354 2011-10-03 21:17:37,230: Managing services: [<cm.services.apps.postgres.PostgresService object at 0x2af8290>] [INFO] postgres:24 2011-10-03 21:17:37,230: Removing 'Postgres' service [DEBUG] misc:511 2011-10-03 21:17:37,289: Successfully set ownership of Postgres data directory [INFO] postgres:102 2011-10-03 21:17:37,290: Stopping PostgreSQL... [ERROR] misc:514 2011-10-03 21:17:37,325: Encountered problem while stopping PostgreSQL, running command '/bin/su - postgres -c "/usr/lib/postgresql/8.4/bin/pg_ctl -w -D /mnt/galaxyData/pgsql/data -o\"-p 5840\" stop"' returned code '1' and following stderr: 'pg_ctl: PID file "/mnt/galaxyData/pgsql/data/postmaster.pid" does not exist Is server running? ' [DEBUG] root:354 2011-10-03 21:17:37,887: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:17:37,888: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:17:37,888: Shutting down Galaxy... [ERROR] misc:514 2011-10-03 21:17:38,244: Error stopping Galaxy, running command '/bin/su - galaxy -c "sh $GALAXY_HOME/run.sh --stop-daemon"' returned code '1' and following stderr: '' [ERROR] postgres:138 2011-10-03 21:17:44,686: PostgreSQL daemon NOT running. [DEBUG] master:1510 2011-10-03 21:17:44,686: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Error; Galaxy..Shutting down; Python version: (2, 6) [DEBUG] app:42 2011-10-03 21:18:47,413: Initializing app [DEBUG] ec2:207 2011-10-03 21:18:47,413: Getting boto S3 connection [DEBUG] ec2:209 2011-10-03 21:18:47,413: No S3 Connection, creating a new one. [DEBUG] ec2:212 2011-10-03 21:18:47,413: Got boto S3 connection. [INFO] misc:378 2011-10-03 21:18:47,495: Retrieved file 'persistent_data.yaml' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to 'pd.yaml'. [INFO] app:52 2011-10-03 21:18:47,501: Master starting [DEBUG] master:50 2011-10-03 21:18:47,604: Initializing console manager - cluster start time: 2011-10-03 21:18:47.604445 [DEBUG] connection:648 2011-10-03 21:18:47,606: Start from server, version: 8.0, properties: {u'platform': 'Erlang/OTP', u'product': 'RabbitMQ', u'version': '1.7.2', u'copyright': 'Copyright (C) 2007-2010 LShift Ltd., Cohesive Financial Technologies LLC., and Rabbit Technologies Ltd.', u'information': 'Licensed under the MPL. See http://www.rabbitmq.com/'}, mechanisms: ['PLAIN', 'AMQPLAIN'], locales: ['en_US'] [DEBUG] connection:494 2011-10-03 21:18:47,646: Open OK! known_hosts [domU-12-31-39-01-61-F2:5672] [DEBUG] channel:70 2011-10-03 21:18:47,646: using channel_id: 1 [DEBUG] channel:484 2011-10-03 21:18:47,647: Channel open [DEBUG] comm:35 2011-10-03 21:18:47,649: Successfully established AMQP connection [DEBUG] master:436 2011-10-03 21:18:47,649: Trying to discover any worker instances associated with this cluster... [DEBUG] ec2:177 2011-10-03 21:18:47,649: Establishing boto EC2 connection [DEBUG] ec2:85 2011-10-03 21:18:47,649: Gathering instance zone, attempt 0 [DEBUG] ec2:90 2011-10-03 21:18:47,652: Instance zone is 'us-east-1a' [DEBUG] ec2:198 2011-10-03 21:18:47,933: Got boto EC2 connection for region 'us-east-1' [DEBUG] ec2:66 2011-10-03 21:18:47,981: Gathering instance id, attempt 0 [DEBUG] ec2:71 2011-10-03 21:18:47,983: Instance ID is 'i-90bed4f0' [DEBUG] ec2:228 2011-10-03 21:18:48,053: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'i-90bed4f0' [DEBUG] ec2:228 2011-10-03 21:18:48,094: Adding tag 'role:master' to resource 'i-90bed4f0' [DEBUG] master:147 2011-10-03 21:18:48,160: ud at manager start: {'access_key': 'AKIAILGV2D5H2XA73EZQ', 'data_filesystems': {'galaxyData': [{'vol_id': 'vol-b53762df', 'size': 600}]}, 'cloudman_home': '/mnt/cm', 'static_filesystems': [{'snap_id': u'snap-5b030634', 'filesystem': 'galaxyIndices', 'size': 700}, {'snap_id': u'snap-1688b978', 'filesystem': 'galaxyTools', 'size': 2}], 'cluster_name': 'CJDGalaxy_Cluster', 'services': [{'service': 'SGE'}, {'service': 'Postgres'}, {'service': 'Galaxy'}], 'bucket_default': 'cloudman', 'boot_script_name': 'cm_boot.py', 'bucket_cluster': 'cm-6d20503431d38fb901ad6a550b90e0d4', 'boot_script_path': '/tmp/cm', 'role': 'master', 'secret_key': 'ARHzUdsBnOVFgT0DE7+X7HXdfQjsZ3m4yFo5Q/S/', 'password': 'oclock'} [DEBUG] master:455 2011-10-03 21:18:48,160: Trying to discover any volumes attached to this instance... [DEBUG] base:55 2011-10-03 21:18:48,165: Enabling 'root' controller, class: CM [DEBUG] buildapp:80 2011-10-03 21:18:48,167: Enabling 'httpexceptions' middleware [DEBUG] buildapp:86 2011-10-03 21:18:48,172: Enabling 'recursive' middleware [DEBUG] buildapp:106 2011-10-03 21:18:48,180: Enabling 'print debug' middleware [DEBUG] buildapp:120 2011-10-03 21:18:48,211: Enabling 'error' middleware [DEBUG] buildapp:130 2011-10-03 21:18:48,211: Enabling 'config' middleware [DEBUG] buildapp:134 2011-10-03 21:18:48,211: Enabling 'x-forwarded-host' middleware Starting server in PID 955. [DEBUG] master:461 2011-10-03 21:18:48,307: Attached volumes: [Volume:vol-73bcf219, Volume:vol-5dbaf437, Volume:vol-ffbaf495, Volume:vol-b53762df, Volume:vol-e77e2c8d, Volume:vol-a37e2cc9] [DEBUG] ec2:237 2011-10-03 21:18:48,307: Getting tag 'cluster_name' on resource 'vol-73bcf219' [DEBUG] ec2:237 2011-10-03 21:18:48,307: Getting tag 'cluster_name' on resource 'vol-5dbaf437' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-ffbaf495' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-b53762df' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-e77e2c8d' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-a37e2cc9' [DEBUG] master:180 2011-10-03 21:18:48,308: Adding static filesystem: 'galaxyIndices' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-73bcf219' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-5dbaf437' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-ffbaf495' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-b53762df' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-e77e2c8d' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-a37e2cc9' [DEBUG] master:180 2011-10-03 21:18:48,310: Adding static filesystem: 'galaxyTools' [DEBUG] master:185 2011-10-03 21:18:48,310: Adding a previously existing data filesystem: 'galaxyData' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'SGE' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'Postgres' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'Galaxy' [INFO] master:155 2011-10-03 21:18:48,310: Completed initial cluster configuration. [DEBUG] master:1488 2011-10-03 21:18:48,310: Monitor started; manager started serving on 0.0.0.0:42284 view at http://127.0.0.1:42284 [DEBUG] master:1515 2011-10-03 21:18:52,314: Monitor adding service 'SGE' [DEBUG] __init__:31 2011-10-03 21:18:52,314: Trying to add service 'SGE' [INFO] __init__:49 2011-10-03 21:18:52,321: Prerequisites OK; starting service 'SGE' [DEBUG] sge:61 2011-10-03 21:18:52,322: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:18:52,352: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:18:53,460: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:18:55,627: Configuring SGE... [DEBUG] ec2:136 2011-10-03 21:18:55,628: Gathering instance private hostname, attempt 0 [DEBUG] sge:104 2011-10-03 21:18:55,630: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:18:55,630: Setting up SGE. [ERROR] misc:514 2011-10-03 21:18:55,848: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] master:1515 2011-10-03 21:18:55,848: Monitor adding service 'FS-galaxyIndices' [DEBUG] filesystem:311 2011-10-03 21:18:55,849: Trying to add service 'FS-galaxyIndices' [DEBUG] filesystem:135 2011-10-03 21:18:55,849: Creating a new volume of size '700' in zone 'us-east-1a' from snapshot 'snap-5b030634' [DEBUG] filesystem:139 2011-10-03 21:19:01,945: Created new volume of size '700' from snapshot 'snap-5b030634' with ID 'vol-0d6b3967' in zone 'us-east-1a' [DEBUG] ec2:228 2011-10-03 21:19:01,946: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-0d6b3967' [DEBUG] ec2:228 2011-10-03 21:19:02,001: Adding tag 'filesystem:galaxyIndices' to resource 'vol-0d6b3967' [DEBUG] filesystem:319 2011-10-03 21:19:02,076: Marked volume 'vol-0d6b3967' from file system 'galaxyIndices' as 'static' [DEBUG] filesystem:129 2011-10-03 21:19:02,130: Running on kernel version 2.6.32-308-ec2; set volume device as '/dev/sdg6' and attach device as '/dev/sdg6' [DEBUG] filesystem:167 2011-10-03 21:19:02,130: Attaching volume 'vol-0d6b3967' to instance 'i-90bed4f0' as device '/dev/sdg6' [DEBUG] filesystem:190 2011-10-03 21:19:02,222: Attaching volume 'vol-0d6b3967'; status: attaching (check 0/30) [DEBUG] filesystem:190 2011-10-03 21:19:04,328: Attaching volume 'vol-0d6b3967'; status: attaching (check 1/30) [DEBUG] filesystem:190 2011-10-03 21:19:06,486: Attaching volume 'vol-0d6b3967'; status: attaching (check 2/30) [DEBUG] filesystem:190 2011-10-03 21:19:08,566: Attaching volume 'vol-0d6b3967'; status: attaching (check 3/30) [DEBUG] filesystem:190 2011-10-03 21:19:10,624: Attaching volume 'vol-0d6b3967'; status: attaching (check 4/30) [DEBUG] filesystem:190 2011-10-03 21:19:12,763: Attaching volume 'vol-0d6b3967'; status: attached (check 5/30) [DEBUG] filesystem:192 2011-10-03 21:19:12,764: Volume 'vol-0d6b3967' attached to instance 'i-90bed4f0' as device '/dev/sdg6' [DEBUG] filesystem:426 2011-10-03 21:19:12,832: Path '/dev/sdg6' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:14,066: Successfully mounted file system '/mnt/galaxyIndices' from '/dev/sdg6' [DEBUG] misc:511 2011-10-03 21:19:14,074: Successfully edited '/mnt/galaxyIndices' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:15,161: As part of filesystem 'Filesystem-galaxyIndices' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:15,237: Monitor adding service 'FS-galaxyTools' [DEBUG] filesystem:311 2011-10-03 21:19:15,237: Trying to add service 'FS-galaxyTools' [DEBUG] filesystem:135 2011-10-03 21:19:15,238: Creating a new volume of size '2' in zone 'us-east-1a' from snapshot 'snap-1688b978' [DEBUG] filesystem:139 2011-10-03 21:19:15,671: Created new volume of size '2' from snapshot 'snap-1688b978' with ID 'vol-c56b39af' in zone 'us-east-1a' [DEBUG] ec2:228 2011-10-03 21:19:15,671: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-c56b39af' [DEBUG] ec2:228 2011-10-03 21:19:15,731: Adding tag 'filesystem:galaxyTools' to resource 'vol-c56b39af' [DEBUG] filesystem:319 2011-10-03 21:19:15,778: Marked volume 'vol-c56b39af' from file system 'galaxyTools' as 'static' [DEBUG] filesystem:129 2011-10-03 21:19:15,828: Running on kernel version 2.6.32-308-ec2; set volume device as '/dev/sdg7' and attach device as '/dev/sdg7' [DEBUG] filesystem:167 2011-10-03 21:19:15,828: Attaching volume 'vol-c56b39af' to instance 'i-90bed4f0' as device '/dev/sdg7' [DEBUG] filesystem:190 2011-10-03 21:19:15,920: Attaching volume 'vol-c56b39af'; status: attaching (check 0/30) [DEBUG] filesystem:190 2011-10-03 21:19:18,051: Attaching volume 'vol-c56b39af'; status: attaching (check 1/30) [DEBUG] filesystem:190 2011-10-03 21:19:20,200: Attaching volume 'vol-c56b39af'; status: attaching (check 2/30) [DEBUG] filesystem:190 2011-10-03 21:19:22,259: Attaching volume 'vol-c56b39af'; status: attaching (check 3/30) [DEBUG] filesystem:190 2011-10-03 21:19:24,308: Attaching volume 'vol-c56b39af'; status: attaching (check 4/30) [DEBUG] filesystem:190 2011-10-03 21:19:26,506: Attaching volume 'vol-c56b39af'; status: attached (check 5/30) [DEBUG] filesystem:192 2011-10-03 21:19:26,507: Volume 'vol-c56b39af' attached to instance 'i-90bed4f0' as device '/dev/sdg7' [DEBUG] filesystem:426 2011-10-03 21:19:26,554: Path '/dev/sdg7' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:27,482: Successfully mounted file system '/mnt/galaxyTools' from '/dev/sdg7' [DEBUG] misc:511 2011-10-03 21:19:27,489: Successfully edited '/mnt/galaxyTools' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:28,726: As part of filesystem 'Filesystem-galaxyTools' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:28,825: Monitor adding service 'FS-galaxyData' [DEBUG] filesystem:311 2011-10-03 21:19:28,826: Trying to add service 'FS-galaxyData' [DEBUG] filesystem:143 2011-10-03 21:19:28,950: Tried to create a volume but it is in state 'attached' (volume ID: vol-b53762df) [DEBUG] ec2:228 2011-10-03 21:19:28,950: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-b53762df' [DEBUG] ec2:228 2011-10-03 21:19:28,995: Adding tag 'filesystem:galaxyData' to resource 'vol-b53762df' [DEBUG] filesystem:214 2011-10-03 21:19:29,164: Tried to attach a volume but the volume 'vol-b53762df' is already attached (as device /dev/sdg3) [DEBUG] filesystem:426 2011-10-03 21:19:29,249: Path '/dev/sdg3' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:29,690: Successfully mounted file system '/mnt/galaxyData' from '/dev/sdg3' [DEBUG] misc:511 2011-10-03 21:19:29,702: Successfully edited '/mnt/galaxyData' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:30,804: As part of filesystem 'Filesystem-galaxyData' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:30,854: Monitor adding service 'Postgres' [DEBUG] __init__:31 2011-10-03 21:19:30,855: Trying to add service 'Postgres' [DEBUG] __init__:36 2011-10-03 21:19:30,855: 'Postgres' service checking its prerequisite 'Filesystem:galaxyData' [INFO] __init__:49 2011-10-03 21:19:30,855: Prerequisites OK; starting service 'Postgres' [DEBUG] misc:511 2011-10-03 21:19:31,057: Successfully set ownership of Postgres data directory [ERROR] postgres:138 2011-10-03 21:19:31,058: PostgreSQL daemon NOT running. [ERROR] postgres:138 2011-10-03 21:19:31,058: PostgreSQL daemon NOT running. [INFO] postgres:90 2011-10-03 21:19:31,058: Starting PostgreSQL... [DEBUG] misc:511 2011-10-03 21:19:31,079: Successfully changed owner of postgres data dir [DEBUG] misc:511 2011-10-03 21:19:32,218: Successfully started PostgreSQL server [INFO] postgres:95 2011-10-03 21:19:32,332: Successfully started PostgreSQL. [DEBUG] master:1515 2011-10-03 21:19:32,332: Monitor adding service 'Galaxy' [DEBUG] __init__:31 2011-10-03 21:19:32,332: Trying to add service 'Galaxy' [DEBUG] __init__:36 2011-10-03 [ERROR] misc:514 2011-10-03 20:55:37,222: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 20:55:37,223: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 20:55:37,223: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 20:55:38,059: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 20:55:39,657: Configuring SGE... [DEBUG] sge:104 2011-10-03 20:55:39,658: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 20:55:39,659: Setting up SGE. [ERROR] misc:514 2011-10-03 20:55:39,769: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] galaxy:139 2011-10-03 20:55:47,615: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:55:47,616: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:04,183: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:04,184: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:20,481: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:20,481: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:36,769: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:36,770: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:56:53,039: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:56:53,039: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:09,346: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:09,346: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:25,641: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:25,642: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:41,944: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:41,944: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:57:58,246: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:57:58,247: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:14,523: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:14,523: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:30,819: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:30,820: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:58:47,089: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:58:47,089: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:03,385: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:03,386: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:19,713: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:19,713: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:35,996: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:35,996: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 20:59:52,264: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 20:59:52,265: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:08,545: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:08,545: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:24,824: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:24,825: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:41,116: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:41,117: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:00:57,398: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:00:57,398: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:13,676: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:13,677: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:29,993: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:29,994: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:01:46,312: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:01:46,313: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:02,642: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:02,643: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:18,934: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:18,934: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [INFO] sge:28 2011-10-03 21:02:19,073: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:19,079: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 21:02:19,080: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:02:19,080: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:02:19,779: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:02:21,313: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:02:21,314: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:02:21,314: Setting up SGE. [ERROR] misc:514 2011-10-03 21:02:21,424: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] root:354 2011-10-03 21:02:30,686: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:02:30,687: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:30,692: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [INFO] sge:28 2011-10-03 21:02:31,978: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:31,983: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 21:02:31,984: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:02:31,984: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:02:32,216: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:02:33,718: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:02:33,719: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:02:33,719: Setting up SGE. [ERROR] misc:514 2011-10-03 21:02:33,830: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] galaxy:139 2011-10-03 21:02:35,204: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:35,205: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:51,478: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:51,478: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:07,771: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:07,772: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:24,109: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:24,109: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:40,384: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:40,384: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:56,651: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:56,651: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:12,920: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:12,921: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:29,215: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:29,215: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:45,524: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:45,524: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:01,832: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:01,832: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:18,100: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:18,101: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:34,374: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:34,374: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:50,636: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:50,637: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:06,984: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:06,985: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:23,253: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:23,254: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:39,536: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:39,537: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:55,787: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:55,788: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] root:354 2011-10-03 21:07:09,086: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:07:09,086: Removing SGE service [ERROR] misc:514 2011-10-03 21:07:09,092: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] root:354 2011-10-03 21:07:10,053: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:07:10,053: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:07:10,053: Shutting down Galaxy... [DEBUG] misc:511 2011-10-03 21:07:11,409: Successfully stopped Galaxy. [DEBUG] master:1510 2011-10-03 21:07:12,062: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Shut down; [DEBUG] root:354 2011-10-03 21:07:13,247: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:07:13,247: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:07:13,247: Shutting down Galaxy... [ERROR] misc:514 2011-10-03 21:07:13,594: Error stopping Galaxy, running command '/bin/su - galaxy -c "sh $GALAXY_HOME/run.sh --stop-daemon"' returned code '1' and following stderr: '' [DEBUG] root:354 2011-10-03 21:07:19,796: Managing services: [<cm.services.apps.postgres.PostgresService object at 0x2af8290>] [INFO] postgres:24 2011-10-03 21:07:19,797: Removing 'Postgres' service [DEBUG] misc:511 2011-10-03 21:07:19,863: Successfully set ownership of Postgres data directory [INFO] postgres:102 2011-10-03 21:07:19,864: Stopping PostgreSQL... [DEBUG] misc:511 2011-10-03 21:07:20,910: Successfully stopped PostgreSQL [DEBUG] root:354 2011-10-03 21:07:25,447: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [DEBUG] sge:61 2011-10-03 21:07:25,447: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:07:25,448: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:07:25,617: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:07:27,074: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:07:27,075: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:07:27,075: Setting up SGE. [ERROR] misc:514 2011-10-03 21:07:27,186: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] master:1510 2011-10-03 21:07:28,269: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:07:44,467: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:00,668: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:16,861: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:33,066: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] root:354 2011-10-03 21:08:44,630: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:08:44,631: Removing SGE service [ERROR] misc:514 2011-10-03 21:08:44,636: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] master:1510 2011-10-03 21:08:49,320: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:05,516: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:21,725: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:37,940: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:54,203: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:10,422: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:26,625: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:42,830: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:59,055: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:15,257: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:31,577: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:47,765: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:03,974: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:20,166: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:36,399: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:52,608: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:08,812: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:25,006: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:41,208: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:57,398: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:13,734: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:29,943: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:46,152: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:02,378: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:18,599: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:34,849: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:51,043: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:07,329: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:23,517: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:39,712: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:56,062: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:17:12,268: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:17:28,489: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] root:354 2011-10-03 21:17:36,296: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:17:36,296: Removing SGE service [ERROR] misc:514 2011-10-03 21:17:36,302: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] root:354 2011-10-03 21:17:37,230: Managing services: [<cm.services.apps.postgres.PostgresService object at 0x2af8290>] [INFO] postgres:24 2011-10-03 21:17:37,230: Removing 'Postgres' service [DEBUG] misc:511 2011-10-03 21:17:37,289: Successfully set ownership of Postgres data directory [INFO] postgres:102 2011-10-03 21:17:37,290: Stopping PostgreSQL... [ERROR] misc:514 2011-10-03 21:17:37,325: Encountered problem while stopping PostgreSQL, running command '/bin/su - postgres -c "/usr/lib/postgresql/8.4/bin/pg_ctl -w -D /mnt/galaxyData/pgsql/data -o\"-p 5840\" stop"' returned code '1' and following stderr: 'pg_ctl: PID file "/mnt/galaxyData/pgsql/data/postmaster.pid" does not exist Is server running? ' [DEBUG] root:354 2011-10-03 21:17:37,887: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:17:37,888: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:17:37,888: Shutting down Galaxy... [ERROR] misc:514 2011-10-03 21:17:38,244: Error stopping Galaxy, running command '/bin/su - galaxy -c "sh $GALAXY_HOME/run.sh --stop-daemon"' returned code '1' and following stderr: '' [ERROR] postgres:138 2011-10-03 21:17:44,686: PostgreSQL daemon NOT running. [DEBUG] master:1510 2011-10-03 21:17:44,686: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Error; Galaxy..Shutting down; Python version: (2, 6) [DEBUG] app:42 2011-10-03 21:18:47,413: Initializing app [DEBUG] ec2:207 2011-10-03 21:18:47,413: Getting boto S3 connection [DEBUG] ec2:209 2011-10-03 21:18:47,413: No S3 Connection, creating a new one. [DEBUG] ec2:212 2011-10-03 21:18:47,413: Got boto S3 connection. [INFO] misc:378 2011-10-03 21:18:47,495: Retrieved file 'persistent_data.yaml' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to 'pd.yaml'. [INFO] app:52 2011-10-03 21:18:47,501: Master starting [DEBUG] master:50 2011-10-03 21:18:47,604: Initializing console manager - cluster start time: 2011-10-03 21:18:47.604445 [DEBUG] connection:648 2011-10-03 21:18:47,606: Start from server, version: 8.0, properties: {u'platform': 'Erlang/OTP', u'product': 'RabbitMQ', u'version': '1.7.2', u'copyright': 'Copyright (C) 2007-2010 LShift Ltd., Cohesive Financial Technologies LLC., and Rabbit Technologies Ltd.', u'information': 'Licensed under the MPL. See http://www.rabbitmq.com/'}, mechanisms: ['PLAIN', 'AMQPLAIN'], locales: ['en_US'] [DEBUG] connection:494 2011-10-03 21:18:47,646: Open OK! known_hosts [domU-12-31-39-01-61-F2:5672] [DEBUG] channel:70 2011-10-03 21:18:47,646: using channel_id: 1 [DEBUG] channel:484 2011-10-03 21:18:47,647: Channel open [DEBUG] comm:35 2011-10-03 21:18:47,649: Successfully established AMQP connection [DEBUG] master:436 2011-10-03 21:18:47,649: Trying to discover any worker instances associated with this cluster... [DEBUG] ec2:177 2011-10-03 21:18:47,649: Establishing boto EC2 connection [DEBUG] ec2:85 2011-10-03 21:18:47,649: Gathering instance zone, attempt 0 [DEBUG] ec2:90 2011-10-03 21:18:47,652: Instance zone is 'us-east-1a' [DEBUG] ec2:198 2011-10-03 21:18:47,933: Got boto EC2 connection for region 'us-east-1' [DEBUG] ec2:66 2011-10-03 21:18:47,981: Gathering instance id, attempt 0 [DEBUG] ec2:71 2011-10-03 21:18:47,983: Instance ID is 'i-90bed4f0' [DEBUG] ec2:228 2011-10-03 21:18:48,053: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'i-90bed4f0' [DEBUG] ec2:228 2011-10-03 21:18:48,094: Adding tag 'role:master' to resource 'i-90bed4f0' [DEBUG] master:147 2011-10-03 21:18:48,160: ud at manager start: {'access_key': 'AKIAILGV2D5H2XA73EZQ', 'data_filesystems': {'galaxyData': [{'vol_id': 'vol-b53762df', 'size': 600}]}, 'cloudman_home': '/mnt/cm', 'static_filesystems': [{'snap_id': u'snap-5b030634', 'filesystem': 'galaxyIndices', 'size': 700}, {'snap_id': u'snap-1688b978', 'filesystem': 'galaxyTools', 'size': 2}], 'cluster_name': 'CJDGalaxy_Cluster', 'services': [{'service': 'SGE'}, {'service': 'Postgres'}, {'service': 'Galaxy'}], 'bucket_default': 'cloudman', 'boot_script_name': 'cm_boot.py', 'bucket_cluster': 'cm-6d20503431d38fb901ad6a550b90e0d4', 'boot_script_path': '/tmp/cm', 'role': 'master', 'secret_key': 'ARHzUdsBnOVFgT0DE7+X7HXdfQjsZ3m4yFo5Q/S/', 'password': 'oclock'} [DEBUG] master:455 2011-10-03 21:18:48,160: Trying to discover any volumes attached to this instance... [DEBUG] base:55 2011-10-03 21:18:48,165: Enabling 'root' controller, class: CM [DEBUG] buildapp:80 2011-10-03 21:18:48,167: Enabling 'httpexceptions' middleware [DEBUG] buildapp:86 2011-10-03 21:18:48,172: Enabling 'recursive' middleware [DEBUG] buildapp:106 2011-10-03 21:18:48,180: Enabling 'print debug' middleware [DEBUG] buildapp:120 2011-10-03 21:18:48,211: Enabling 'error' middleware [DEBUG] buildapp:130 2011-10-03 21:18:48,211: Enabling 'config' middleware [DEBUG] buildapp:134 2011-10-03 21:18:48,211: Enabling 'x-forwarded-host' middleware Starting server in PID 955. [DEBUG] master:461 2011-10-03 21:18:48,307: Attached volumes: [Volume:vol-73bcf219, Volume:vol-5dbaf437, Volume:vol-ffbaf495, Volume:vol-b53762df, Volume:vol-e77e2c8d, Volume:vol-a37e2cc9] [DEBUG] ec2:237 2011-10-03 21:18:48,307: Getting tag 'cluster_name' on resource 'vol-73bcf219' [DEBUG] ec2:237 2011-10-03 21:18:48,307: Getting tag 'cluster_name' on resource 'vol-5dbaf437' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-ffbaf495' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-b53762df' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-e77e2c8d' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-a37e2cc9' [DEBUG] master:180 2011-10-03 21:18:48,308: Adding static filesystem: 'galaxyIndices' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-73bcf219' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-5dbaf437' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-ffbaf495' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-b53762df' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-e77e2c8d' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-a37e2cc9' [DEBUG] master:180 2011-10-03 21:18:48,310: Adding static filesystem: 'galaxyTools' [DEBUG] master:185 2011-10-03 21:18:48,310: Adding a previously existing data filesystem: 'galaxyData' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'SGE' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'Postgres' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'Galaxy' [INFO] master:155 2011-10-03 21:18:48,310: Completed initial cluster configuration. [DEBUG] master:1488 2011-10-03 21:18:48,310: Monitor started; manager started serving on 0.0.0.0:42284 view at http://127.0.0.1:42284 [DEBUG] master:1515 2011-10-03 21:18:52,314: Monitor adding service 'SGE' [DEBUG] __init__:31 2011-10-03 21:18:52,314: Trying to add service 'SGE' [INFO] __init__:49 2011-10-03 21:18:52,321: Prerequisites OK; starting service 'SGE' [DEBUG] sge:61 2011-10-03 21:18:52,322: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:18:52,352: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:18:53,460: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:18:55,627: Configuring SGE... [DEBUG] ec2:136 2011-10-03 21:18:55,628: Gathering instance private hostname, attempt 0 [DEBUG] sge:104 2011-10-03 21:18:55,630: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:18:55,630: Setting up SGE. [ERROR] misc:514 2011-10-03 21:18:55,848: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] master:1515 2011-10-03 21:18:55,848: Monitor adding service 'FS-galaxyIndices' [DEBUG] filesystem:311 2011-10-03 21:18:55,849: Trying to add service 'FS-galaxyIndices' [DEBUG] filesystem:135 2011-10-03 21:18:55,849: Creating a new volume of size '700' in zone 'us-east-1a' from snapshot 'snap-5b030634' [DEBUG] filesystem:139 2011-10-03 21:19:01,945: Created new volume of size '700' from snapshot 'snap-5b030634' with ID 'vol-0d6b3967' in zone 'us-east-1a' [DEBUG] ec2:228 2011-10-03 21:19:01,946: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-0d6b3967' [DEBUG] ec2:228 2011-10-03 21:19:02,001: Adding tag 'filesystem:galaxyIndices' to resource 'vol-0d6b3967' [DEBUG] filesystem:319 2011-10-03 21:19:02,076: Marked volume 'vol-0d6b3967' from file system 'galaxyIndices' as 'static' [DEBUG] filesystem:129 2011-10-03 21:19:02,130: Running on kernel version 2.6.32-308-ec2; set volume device as '/dev/sdg6' and attach device as '/dev/sdg6' [DEBUG] filesystem:167 2011-10-03 21:19:02,130: Attaching volume 'vol-0d6b3967' to instance 'i-90bed4f0' as device '/dev/sdg6' [DEBUG] filesystem:190 2011-10-03 21:19:02,222: Attaching volume 'vol-0d6b3967'; status: attaching (check 0/30) [DEBUG] filesystem:190 2011-10-03 21:19:04,328: Attaching volume 'vol-0d6b3967'; status: attaching (check 1/30) [DEBUG] filesystem:190 2011-10-03 21:19:06,486: Attaching volume 'vol-0d6b3967'; status: attaching (check 2/30) [DEBUG] filesystem:190 2011-10-03 21:19:08,566: Attaching volume 'vol-0d6b3967'; status: attaching (check 3/30) [DEBUG] filesystem:190 2011-10-03 21:19:10,624: Attaching volume 'vol-0d6b3967'; status: attaching (check 4/30) [DEBUG] filesystem:190 2011-10-03 21:19:12,763: Attaching volume 'vol-0d6b3967'; status: attached (check 5/30) [DEBUG] filesystem:192 2011-10-03 21:19:12,764: Volume 'vol-0d6b3967' attached to instance 'i-90bed4f0' as device '/dev/sdg6' [DEBUG] filesystem:426 2011-10-03 21:19:12,832: Path '/dev/sdg6' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:14,066: Successfully mounted file system '/mnt/galaxyIndices' from '/dev/sdg6' [DEBUG] misc:511 2011-10-03 21:19:14,074: Successfully edited '/mnt/galaxyIndices' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:15,161: As part of filesystem 'Filesystem-galaxyIndices' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:15,237: Monitor adding service 'FS-galaxyTools' [DEBUG] filesystem:311 2011-10-03 21:19:15,237: Trying to add service 'FS-galaxyTools' [DEBUG] filesystem:135 2011-10-03 21:19:15,238: Creating a new volume of size '2' in zone 'us-east-1a' from snapshot 'snap-1688b978' [DEBUG] filesystem:139 2011-10-03 21:19:15,671: Created new volume of size '2' from snapshot 'snap-1688b978' with ID 'vol-c56b39af' in zone 'us-east-1a' [DEBUG] ec2:228 2011-10-03 21:19:15,671: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-c56b39af' [DEBUG] ec2:228 2011-10-03 21:19:15,731: Adding tag 'filesystem:galaxyTools' to resource 'vol-c56b39af' [DEBUG] filesystem:319 2011-10-03 21:19:15,778: Marked volume 'vol-c56b39af' from file system 'galaxyTools' as 'static' [DEBUG] filesystem:129 2011-10-03 21:19:15,828: Running on kernel version 2.6.32-308-ec2; set volume device as '/dev/sdg7' and attach device as '/dev/sdg7' [DEBUG] filesystem:167 2011-10-03 21:19:15,828: Attaching volume 'vol-c56b39af' to instance 'i-90bed4f0' as device '/dev/sdg7' [DEBUG] filesystem:190 2011-10-03 21:19:15,920: Attaching volume 'vol-c56b39af'; status: attaching (check 0/30) [DEBUG] filesystem:190 2011-10-03 21:19:18,051: Attaching volume 'vol-c56b39af'; status: attaching (check 1/30) [DEBUG] filesystem:190 2011-10-03 21:19:20,200: Attaching volume 'vol-c56b39af'; status: attaching (check 2/30) [DEBUG] filesystem:190 2011-10-03 21:19:22,259: Attaching volume 'vol-c56b39af'; status: attaching (check 3/30) [DEBUG] filesystem:190 2011-10-03 21:19:24,308: Attaching volume 'vol-c56b39af'; status: attaching (check 4/30) [DEBUG] filesystem:190 2011-10-03 21:19:26,506: Attaching volume 'vol-c56b39af'; status: attached (check 5/30) [DEBUG] filesystem:192 2011-10-03 21:19:26,507: Volume 'vol-c56b39af' attached to instance 'i-90bed4f0' as device '/dev/sdg7' [DEBUG] filesystem:426 2011-10-03 21:19:26,554: Path '/dev/sdg7' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:27,482: Successfully mounted file system '/mnt/galaxyTools' from '/dev/sdg7' [DEBUG] misc:511 2011-10-03 21:19:27,489: Successfully edited '/mnt/galaxyTools' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:28,726: As part of filesystem 'Filesystem-galaxyTools' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:28,825: Monitor adding service 'FS-galaxyData' [DEBUG] filesystem:311 2011-10-03 21:19:28,826: Trying to add service 'FS-galaxyData' [DEBUG] filesystem:143 2011-10-03 21:19:28,950: Tried to create a volume but it is in state 'attached' (volume ID: vol-b53762df) [DEBUG] ec2:228 2011-10-03 21:19:28,950: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-b53762df' [DEBUG] ec2:228 2011-10-03 21:19:28,995: Adding tag 'filesystem:galaxyData' to resource 'vol-b53762df' [DEBUG] filesystem:214 2011-10-03 21:19:29,164: Tried to attach a volume but the volume 'vol-b53762df' is already attached (as device /dev/sdg3) [DEBUG] filesystem:426 2011-10-03 21:19:29,249: Path '/dev/sdg3' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:29,690: Successfully mounted file system '/mnt/galaxyData' from '/dev/sdg3' [DEBUG] misc:511 2011-10-03 21:19:29,702: Successfully edited '/mnt/galaxyData' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:30,804: As part of filesystem 'Filesystem-galaxyData' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:30,854: Monitor adding service 'Postgres' [DEBUG] __init__:31 2011-10-03 21:19:30,855: Trying to add service 'Postgres' [DEBUG] __init__:36 2011-10-03 21:19:30,855: 'Postgres' service checking its prerequisite 'Filesystem:galaxyData' [INFO] __init__:49 2011-10-03 21:19:30,855: Prerequisites OK; starting service 'Postgres' [DEBUG] misc:511 2011-10-03 21:19:31,057: Successfully set ownership of Postgres data directory [ERROR] postgres:138 2011-10-03 21:19:31,058: PostgreSQL daemon NOT running. [ERROR] postgres:138 2011-10-03 21:19:31,058: PostgreSQL daemon NOT running. [INFO] postgres:90 2011-10-03 21:19:31,058: Starting PostgreSQL... [DEBUG] misc:511 2011-10-03 21:19:31,079: Successfully changed owner of postgres data dir [DEBUG] misc:511 2011-10-03 21:19:32,218: Successfully started PostgreSQL server [INFO] postgres:95 2011-10-03 21:19:32,332: Successfully started PostgreSQL. [DEBUG] master:1515 2011-10-03 21:19:32,332: Monitor adding service 'Galaxy' [DEBUG] __init__:31 2011-10-03 21:19:32,332: Trying to add service 'Galaxy' [DEBUG] __init__:36 2011-10-03 21:19:32,333: 'Galaxy' service checking its prerequisite 'Postgres:None' [DEBUG] __init__:36 2011-10-03 21:19:32,333: 'Galaxy' service checking its prerequisite 'Filesystem:galaxyTools' [INFO] __init__:49 2011-10-03 21:19:32,333: Prerequisites OK; starting service 'Galaxy' [INFO] galaxy:50 2011-10-03 21:19:32,333: Setting up Galaxy application [DEBUG] ec2:207 2011-10-03 21:19:32,333: Getting boto S3 connection [INFO] misc:378 2011-10-03 21:19:32,943: Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. [INFO] misc:378 2011-10-03 21:19:34,459: Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. [INFO] misc:378 2011-10-03 21:19:34,565: Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. [DEBUG] misc:511 2011-10-03 21:19:36,238: Started FTP server [INFO] galaxy:113 2011-10-03 21:19:36,238: Starting Galaxy... [DEBUG] misc:511 2011-10-03 21:19:43,828: Successfully initiated Galaxy start. [DEBUG] galaxy:139 2011-10-03 21:19:43,852: Galaxy UI does not seem to be accessible. [DEBUG] ec2:207 2011-10-03 21:19:43,852: Getting boto S3 connection [INFO] misc:394 2011-10-03 21:19:44,143: Saved file 'persistent_data.yaml' to bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' [DEBUG] master:1462 2011-10-03 21:19:44,195: Instance post start script (/mnt/cm/post_start_script) does not exist? [DEBUG] galaxy:139 2011-10-03 21:19:48,544: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:19:48,545: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:04,821: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:04,822: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:21,089: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:21,089: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:37,369: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:37,370: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; 21:19:32,333: 'Galaxy' service checking its prerequisite 'Postgres:None' [DEBUG] __init__:36 2011-10-03 21:19:32,333: 'Galaxy' service checking its prerequisite 'Filesystem:galaxyTools' [INFO] __init__:49 2011-10-03 21:19:32,333: Prerequisites OK; starting service 'Galaxy' [INFO] galaxy:50 2011-10-03 21:19:32,333: Setting up Galaxy application [DEBUG] ec2:207 2011-10-03 21:19:32,333: Getting boto S3 connection [INFO] misc:378 2011-10-03 21:19:32,943: Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. [INFO] misc:378 2011-10-03 21:19:34,459: Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. [INFO] misc:378 2011-10-03 21:19:34,565: Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. [DEBUG] misc:511 2011-10-03 21:19:36,238: Started FTP server [INFO] galaxy:113 2011-10-03 21:19:36,238: Starting Galaxy... [DEBUG] misc:511 2011-10-03 21:19:43,828: Successfully initiated Galaxy start. [DEBUG] galaxy:139 2011-10-03 21:19:43,852: Galaxy UI does not seem to be accessible. [DEBUG] ec2:207 2011-10-03 21:19:43,852: Getting boto S3 connection [INFO] misc:394 2011-10-03 21:19:44,143: Saved file 'persistent_data.yaml' to bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' [DEBUG] master:1462 2011-10-03 21:19:44,195: Instance post start script (/mnt/cm/post_start_script) does not exist? [DEBUG] galaxy:139 2011-10-03 21:19:48,544: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:19:48,545: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:04,821: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:04,822: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:21,089: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:21,089: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:37,369: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:37,370: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; 21,313: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:02:21,314: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:02:21,314: Setting up SGE. [ERROR] misc:514 2011-10-03 21:02:21,424: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] root:354 2011-10-03 21:02:30,686: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:02:30,687: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:30,692: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [INFO] sge:28 2011-10-03 21:02:31,978: Removing SGE service [ERROR] misc:514 2011-10-03 21:02:31,983: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] sge:61 2011-10-03 21:02:31,984: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:02:31,984: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:02:32,216: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:02:33,718: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:02:33,719: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:02:33,719: Setting up SGE. [ERROR] misc:514 2011-10-03 21:02:33,830: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] galaxy:139 2011-10-03 21:02:35,204: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:35,205: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:02:51,478: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:02:51,478: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:07,771: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:07,772: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:24,109: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:24,109: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:40,384: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:40,384: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:03:56,651: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:03:56,651: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:12,920: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:12,921: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:29,215: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:29,215: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:04:45,524: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:04:45,524: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:01,832: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:01,832: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:18,100: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:18,101: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:34,374: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:34,374: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:05:50,636: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:05:50,637: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:06,984: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:06,985: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:23,253: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:23,254: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:39,536: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:39,537: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:06:55,787: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:06:55,788: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] root:354 2011-10-03 21:07:09,086: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:07:09,086: Removing SGE service [ERROR] misc:514 2011-10-03 21:07:09,092: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] root:354 2011-10-03 21:07:10,053: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:07:10,053: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:07:10,053: Shutting down Galaxy... [DEBUG] misc:511 2011-10-03 21:07:11,409: Successfully stopped Galaxy. [DEBUG] master:1510 2011-10-03 21:07:12,062: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Shut down; [DEBUG] root:354 2011-10-03 21:07:13,247: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:07:13,247: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:07:13,247: Shutting down Galaxy... [ERROR] misc:514 2011-10-03 21:07:13,594: Error stopping Galaxy, running command '/bin/su - galaxy -c "sh $GALAXY_HOME/run.sh --stop-daemon"' returned code '1' and following stderr: '' [DEBUG] root:354 2011-10-03 21:07:19,796: Managing services: [<cm.services.apps.postgres.PostgresService object at 0x2af8290>] [INFO] postgres:24 2011-10-03 21:07:19,797: Removing 'Postgres' service [DEBUG] misc:511 2011-10-03 21:07:19,863: Successfully set ownership of Postgres data directory [INFO] postgres:102 2011-10-03 21:07:19,864: Stopping PostgreSQL... [DEBUG] misc:511 2011-10-03 21:07:20,910: Successfully stopped PostgreSQL [DEBUG] root:354 2011-10-03 21:07:25,447: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [DEBUG] sge:61 2011-10-03 21:07:25,447: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:07:25,448: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:07:25,617: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:07:27,074: Configuring SGE... [DEBUG] sge:104 2011-10-03 21:07:27,075: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:07:27,075: Setting up SGE. [ERROR] misc:514 2011-10-03 21:07:27,186: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] master:1510 2011-10-03 21:07:28,269: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:07:44,467: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:00,668: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:16,861: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:08:33,066: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] root:354 2011-10-03 21:08:44,630: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:08:44,631: Removing SGE service [ERROR] misc:514 2011-10-03 21:08:44,636: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] master:1510 2011-10-03 21:08:49,320: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:05,516: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:21,725: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:37,940: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:09:54,203: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:10,422: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:26,625: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:42,830: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:10:59,055: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:15,257: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:31,577: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:11:47,765: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:03,974: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:20,166: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:36,399: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:12:52,608: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:08,812: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:25,006: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:41,208: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:13:57,398: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:13,734: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:29,943: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:14:46,152: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:02,378: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:18,599: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:34,849: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:15:51,043: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:07,329: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:23,517: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:39,712: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:16:56,062: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:17:12,268: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] master:1510 2011-10-03 21:17:28,489: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Shut down; Galaxy..Shutting down; [DEBUG] root:354 2011-10-03 21:17:36,296: Managing services: [<cm.services.apps.sge.SGEService object at 0x2904f90>] [INFO] sge:28 2011-10-03 21:17:36,296: Removing SGE service [ERROR] misc:514 2011-10-03 21:17:36,302: Problems stopping SGE master, running command 'export SGE_ROOT=/opt/sge; . $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf -km' returned code '2' and following stderr: '.: 1: Can't open /opt/sge/default/common/settings.sh ' [DEBUG] root:354 2011-10-03 21:17:37,230: Managing services: [<cm.services.apps.postgres.PostgresService object at 0x2af8290>] [INFO] postgres:24 2011-10-03 21:17:37,230: Removing 'Postgres' service [DEBUG] misc:511 2011-10-03 21:17:37,289: Successfully set ownership of Postgres data directory [INFO] postgres:102 2011-10-03 21:17:37,290: Stopping PostgreSQL... [ERROR] misc:514 2011-10-03 21:17:37,325: Encountered problem while stopping PostgreSQL, running command '/bin/su - postgres -c "/usr/lib/postgresql/8.4/bin/pg_ctl -w -D /mnt/galaxyData/pgsql/data -o\"-p 5840\" stop"' returned code '1' and following stderr: 'pg_ctl: PID file "/mnt/galaxyData/pgsql/data/postmaster.pid" does not exist Is server running? ' [DEBUG] root:354 2011-10-03 21:17:37,887: Managing services: [<cm.services.apps.galaxy.GalaxyService object at 0x2af8250>] [INFO] galaxy:30 2011-10-03 21:17:37,888: Removing 'Galaxy' service [INFO] galaxy:122 2011-10-03 21:17:37,888: Shutting down Galaxy... [ERROR] misc:514 2011-10-03 21:17:38,244: Error stopping Galaxy, running command '/bin/su - galaxy -c "sh $GALAXY_HOME/run.sh --stop-daemon"' returned code '1' and following stderr: '' [ERROR] postgres:138 2011-10-03 21:17:44,686: PostgreSQL daemon NOT running. [DEBUG] master:1510 2011-10-03 21:17:44,686: S&S: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..Error; Galaxy..Shutting down; Python version: (2, 6) [DEBUG] app:42 2011-10-03 21:18:47,413: Initializing app [DEBUG] ec2:207 2011-10-03 21:18:47,413: Getting boto S3 connection [DEBUG] ec2:209 2011-10-03 21:18:47,413: No S3 Connection, creating a new one. [DEBUG] ec2:212 2011-10-03 21:18:47,413: Got boto S3 connection. [INFO] misc:378 2011-10-03 21:18:47,495: Retrieved file 'persistent_data.yaml' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to 'pd.yaml'. [INFO] app:52 2011-10-03 21:18:47,501: Master starting [DEBUG] master:50 2011-10-03 21:18:47,604: Initializing console manager - cluster start time: 2011-10-03 21:18:47.604445 [DEBUG] connection:648 2011-10-03 21:18:47,606: Start from server, version: 8.0, properties: {u'platform': 'Erlang/OTP', u'product': 'RabbitMQ', u'version': '1.7.2', u'copyright': 'Copyright (C) 2007-2010 LShift Ltd., Cohesive Financial Technologies LLC., and Rabbit Technologies Ltd.', u'information': 'Licensed under the MPL. See http://www.rabbitmq.com/'}, mechanisms: ['PLAIN', 'AMQPLAIN'], locales: ['en_US'] [DEBUG] connection:494 2011-10-03 21:18:47,646: Open OK! known_hosts [domU-12-31-39-01-61-F2:5672] [DEBUG] channel:70 2011-10-03 21:18:47,646: using channel_id: 1 [DEBUG] channel:484 2011-10-03 21:18:47,647: Channel open [DEBUG] comm:35 2011-10-03 21:18:47,649: Successfully established AMQP connection [DEBUG] master:436 2011-10-03 21:18:47,649: Trying to discover any worker instances associated with this cluster... [DEBUG] ec2:177 2011-10-03 21:18:47,649: Establishing boto EC2 connection [DEBUG] ec2:85 2011-10-03 21:18:47,649: Gathering instance zone, attempt 0 [DEBUG] ec2:90 2011-10-03 21:18:47,652: Instance zone is 'us-east-1a' [DEBUG] ec2:198 2011-10-03 21:18:47,933: Got boto EC2 connection for region 'us-east-1' [DEBUG] ec2:66 2011-10-03 21:18:47,981: Gathering instance id, attempt 0 [DEBUG] ec2:71 2011-10-03 21:18:47,983: Instance ID is 'i-90bed4f0' [DEBUG] ec2:228 2011-10-03 21:18:48,053: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'i-90bed4f0' [DEBUG] ec2:228 2011-10-03 21:18:48,094: Adding tag 'role:master' to resource 'i-90bed4f0' [DEBUG] master:147 2011-10-03 21:18:48,160: ud at manager start: {'access_key': 'AKIAILGV2D5H2XA73EZQ', 'data_filesystems': {'galaxyData': [{'vol_id': 'vol-b53762df', 'size': 600}]}, 'cloudman_home': '/mnt/cm', 'static_filesystems': [{'snap_id': u'snap-5b030634', 'filesystem': 'galaxyIndices', 'size': 700}, {'snap_id': u'snap-1688b978', 'filesystem': 'galaxyTools', 'size': 2}], 'cluster_name': 'CJDGalaxy_Cluster', 'services': [{'service': 'SGE'}, {'service': 'Postgres'}, {'service': 'Galaxy'}], 'bucket_default': 'cloudman', 'boot_script_name': 'cm_boot.py', 'bucket_cluster': 'cm-6d20503431d38fb901ad6a550b90e0d4', 'boot_script_path': '/tmp/cm', 'role': 'master', 'secret_key': 'ARHzUdsBnOVFgT0DE7+X7HXdfQjsZ3m4yFo5Q/S/', 'password': 'oclock'} [DEBUG] master:455 2011-10-03 21:18:48,160: Trying to discover any volumes attached to this instance... [DEBUG] base:55 2011-10-03 21:18:48,165: Enabling 'root' controller, class: CM [DEBUG] buildapp:80 2011-10-03 21:18:48,167: Enabling 'httpexceptions' middleware [DEBUG] buildapp:86 2011-10-03 21:18:48,172: Enabling 'recursive' middleware [DEBUG] buildapp:106 2011-10-03 21:18:48,180: Enabling 'print debug' middleware [DEBUG] buildapp:120 2011-10-03 21:18:48,211: Enabling 'error' middleware [DEBUG] buildapp:130 2011-10-03 21:18:48,211: Enabling 'config' middleware [DEBUG] buildapp:134 2011-10-03 21:18:48,211: Enabling 'x-forwarded-host' middleware Starting server in PID 955. [DEBUG] master:461 2011-10-03 21:18:48,307: Attached volumes: [Volume:vol-73bcf219, Volume:vol-5dbaf437, Volume:vol-ffbaf495, Volume:vol-b53762df, Volume:vol-e77e2c8d, Volume:vol-a37e2cc9] [DEBUG] ec2:237 2011-10-03 21:18:48,307: Getting tag 'cluster_name' on resource 'vol-73bcf219' [DEBUG] ec2:237 2011-10-03 21:18:48,307: Getting tag 'cluster_name' on resource 'vol-5dbaf437' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-ffbaf495' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-b53762df' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-e77e2c8d' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-a37e2cc9' [DEBUG] master:180 2011-10-03 21:18:48,308: Adding static filesystem: 'galaxyIndices' [DEBUG] ec2:237 2011-10-03 21:18:48,308: Getting tag 'cluster_name' on resource 'vol-73bcf219' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-5dbaf437' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-ffbaf495' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-b53762df' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-e77e2c8d' [DEBUG] ec2:237 2011-10-03 21:18:48,309: Getting tag 'cluster_name' on resource 'vol-a37e2cc9' [DEBUG] master:180 2011-10-03 21:18:48,310: Adding static filesystem: 'galaxyTools' [DEBUG] master:185 2011-10-03 21:18:48,310: Adding a previously existing data filesystem: 'galaxyData' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'SGE' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'Postgres' [DEBUG] master:193 2011-10-03 21:18:48,310: Adding service: 'Galaxy' [INFO] master:155 2011-10-03 21:18:48,310: Completed initial cluster configuration. [DEBUG] master:1488 2011-10-03 21:18:48,310: Monitor started; manager started serving on 0.0.0.0:42284 view at http://127.0.0.1:42284 [DEBUG] master:1515 2011-10-03 21:18:52,314: Monitor adding service 'SGE' [DEBUG] __init__:31 2011-10-03 21:18:52,314: Trying to add service 'SGE' [INFO] __init__:49 2011-10-03 21:18:52,321: Prerequisites OK; starting service 'SGE' [DEBUG] sge:61 2011-10-03 21:18:52,322: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-10-03 21:18:52,352: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-03 21:18:53,460: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-03 21:18:55,627: Configuring SGE... [DEBUG] ec2:136 2011-10-03 21:18:55,628: Gathering instance private hostname, attempt 0 [DEBUG] sge:104 2011-10-03 21:18:55,630: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-03 21:18:55,630: Setting up SGE. [ERROR] misc:514 2011-10-03 21:18:55,848: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) ' [DEBUG] master:1515 2011-10-03 21:18:55,848: Monitor adding service 'FS-galaxyIndices' [DEBUG] filesystem:311 2011-10-03 21:18:55,849: Trying to add service 'FS-galaxyIndices' [DEBUG] filesystem:135 2011-10-03 21:18:55,849: Creating a new volume of size '700' in zone 'us-east-1a' from snapshot 'snap-5b030634' [DEBUG] filesystem:139 2011-10-03 21:19:01,945: Created new volume of size '700' from snapshot 'snap-5b030634' with ID 'vol-0d6b3967' in zone 'us-east-1a' [DEBUG] ec2:228 2011-10-03 21:19:01,946: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-0d6b3967' [DEBUG] ec2:228 2011-10-03 21:19:02,001: Adding tag 'filesystem:galaxyIndices' to resource 'vol-0d6b3967' [DEBUG] filesystem:319 2011-10-03 21:19:02,076: Marked volume 'vol-0d6b3967' from file system 'galaxyIndices' as 'static' [DEBUG] filesystem:129 2011-10-03 21:19:02,130: Running on kernel version 2.6.32-308-ec2; set volume device as '/dev/sdg6' and attach device as '/dev/sdg6' [DEBUG] filesystem:167 2011-10-03 21:19:02,130: Attaching volume 'vol-0d6b3967' to instance 'i-90bed4f0' as device '/dev/sdg6' [DEBUG] filesystem:190 2011-10-03 21:19:02,222: Attaching volume 'vol-0d6b3967'; status: attaching (check 0/30) [DEBUG] filesystem:190 2011-10-03 21:19:04,328: Attaching volume 'vol-0d6b3967'; status: attaching (check 1/30) [DEBUG] filesystem:190 2011-10-03 21:19:06,486: Attaching volume 'vol-0d6b3967'; status: attaching (check 2/30) [DEBUG] filesystem:190 2011-10-03 21:19:08,566: Attaching volume 'vol-0d6b3967'; status: attaching (check 3/30) [DEBUG] filesystem:190 2011-10-03 21:19:10,624: Attaching volume 'vol-0d6b3967'; status: attaching (check 4/30) [DEBUG] filesystem:190 2011-10-03 21:19:12,763: Attaching volume 'vol-0d6b3967'; status: attached (check 5/30) [DEBUG] filesystem:192 2011-10-03 21:19:12,764: Volume 'vol-0d6b3967' attached to instance 'i-90bed4f0' as device '/dev/sdg6' [DEBUG] filesystem:426 2011-10-03 21:19:12,832: Path '/dev/sdg6' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:14,066: Successfully mounted file system '/mnt/galaxyIndices' from '/dev/sdg6' [DEBUG] misc:511 2011-10-03 21:19:14,074: Successfully edited '/mnt/galaxyIndices' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:15,161: As part of filesystem 'Filesystem-galaxyIndices' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:15,237: Monitor adding service 'FS-galaxyTools' [DEBUG] filesystem:311 2011-10-03 21:19:15,237: Trying to add service 'FS-galaxyTools' [DEBUG] filesystem:135 2011-10-03 21:19:15,238: Creating a new volume of size '2' in zone 'us-east-1a' from snapshot 'snap-1688b978' [DEBUG] filesystem:139 2011-10-03 21:19:15,671: Created new volume of size '2' from snapshot 'snap-1688b978' with ID 'vol-c56b39af' in zone 'us-east-1a' [DEBUG] ec2:228 2011-10-03 21:19:15,671: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-c56b39af' [DEBUG] ec2:228 2011-10-03 21:19:15,731: Adding tag 'filesystem:galaxyTools' to resource 'vol-c56b39af' [DEBUG] filesystem:319 2011-10-03 21:19:15,778: Marked volume 'vol-c56b39af' from file system 'galaxyTools' as 'static' [DEBUG] filesystem:129 2011-10-03 21:19:15,828: Running on kernel version 2.6.32-308-ec2; set volume device as '/dev/sdg7' and attach device as '/dev/sdg7' [DEBUG] filesystem:167 2011-10-03 21:19:15,828: Attaching volume 'vol-c56b39af' to instance 'i-90bed4f0' as device '/dev/sdg7' [DEBUG] filesystem:190 2011-10-03 21:19:15,920: Attaching volume 'vol-c56b39af'; status: attaching (check 0/30) [DEBUG] filesystem:190 2011-10-03 21:19:18,051: Attaching volume 'vol-c56b39af'; status: attaching (check 1/30) [DEBUG] filesystem:190 2011-10-03 21:19:20,200: Attaching volume 'vol-c56b39af'; status: attaching (check 2/30) [DEBUG] filesystem:190 2011-10-03 21:19:22,259: Attaching volume 'vol-c56b39af'; status: attaching (check 3/30) [DEBUG] filesystem:190 2011-10-03 21:19:24,308: Attaching volume 'vol-c56b39af'; status: attaching (check 4/30) [DEBUG] filesystem:190 2011-10-03 21:19:26,506: Attaching volume 'vol-c56b39af'; status: attached (check 5/30) [DEBUG] filesystem:192 2011-10-03 21:19:26,507: Volume 'vol-c56b39af' attached to instance 'i-90bed4f0' as device '/dev/sdg7' [DEBUG] filesystem:426 2011-10-03 21:19:26,554: Path '/dev/sdg7' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:27,482: Successfully mounted file system '/mnt/galaxyTools' from '/dev/sdg7' [DEBUG] misc:511 2011-10-03 21:19:27,489: Successfully edited '/mnt/galaxyTools' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:28,726: As part of filesystem 'Filesystem-galaxyTools' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:28,825: Monitor adding service 'FS-galaxyData' [DEBUG] filesystem:311 2011-10-03 21:19:28,826: Trying to add service 'FS-galaxyData' [DEBUG] filesystem:143 2011-10-03 21:19:28,950: Tried to create a volume but it is in state 'attached' (volume ID: vol-b53762df) [DEBUG] ec2:228 2011-10-03 21:19:28,950: Adding tag 'clusterName:CJDGalaxy_Cluster' to resource 'vol-b53762df' [DEBUG] ec2:228 2011-10-03 21:19:28,995: Adding tag 'filesystem:galaxyData' to resource 'vol-b53762df' [DEBUG] filesystem:214 2011-10-03 21:19:29,164: Tried to attach a volume but the volume 'vol-b53762df' is already attached (as device /dev/sdg3) [DEBUG] filesystem:426 2011-10-03 21:19:29,249: Path '/dev/sdg3' checked and exists. [DEBUG] misc:511 2011-10-03 21:19:29,690: Successfully mounted file system '/mnt/galaxyData' from '/dev/sdg3' [DEBUG] misc:511 2011-10-03 21:19:29,702: Successfully edited '/mnt/galaxyData' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-03 21:19:30,804: As part of filesystem 'Filesystem-galaxyData' update, successfully restarted NFS server [DEBUG] master:1515 2011-10-03 21:19:30,854: Monitor adding service 'Postgres' [DEBUG] __init__:31 2011-10-03 21:19:30,855: Trying to add service 'Postgres' [DEBUG] __init__:36 2011-10-03 21:19:30,855: 'Postgres' service checking its prerequisite 'Filesystem:galaxyData' [INFO] __init__:49 2011-10-03 21:19:30,855: Prerequisites OK; starting service 'Postgres' [DEBUG] misc:511 2011-10-03 21:19:31,057: Successfully set ownership of Postgres data directory [ERROR] postgres:138 2011-10-03 21:19:31,058: PostgreSQL daemon NOT running. [ERROR] postgres:138 2011-10-03 21:19:31,058: PostgreSQL daemon NOT running. [INFO] postgres:90 2011-10-03 21:19:31,058: Starting PostgreSQL... [DEBUG] misc:511 2011-10-03 21:19:31,079: Successfully changed owner of postgres data dir [DEBUG] misc:511 2011-10-03 21:19:32,218: Successfully started PostgreSQL server [INFO] postgres:95 2011-10-03 21:19:32,332: Successfully started PostgreSQL. [DEBUG] master:1515 2011-10-03 21:19:32,332: Monitor adding service 'Galaxy' [DEBUG] __init__:31 2011-10-03 21:19:32,332: Trying to add service 'Galaxy' [DEBUG] __init__:36 2011-10-03 21:19:32,333: 'Galaxy' service checking its prerequisite 'Postgres:None' [DEBUG] __init__:36 2011-10-03 21:19:32,333: 'Galaxy' service checking its prerequisite 'Filesystem:galaxyTools' [INFO] __init__:49 2011-10-03 21:19:32,333: Prerequisites OK; starting service 'Galaxy' [INFO] galaxy:50 2011-10-03 21:19:32,333: Setting up Galaxy application [DEBUG] ec2:207 2011-10-03 21:19:32,333: Getting boto S3 connection [INFO] misc:378 2011-10-03 21:19:32,943: Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. [INFO] misc:378 2011-10-03 21:19:34,459: Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. [INFO] misc:378 2011-10-03 21:19:34,565: Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. [DEBUG] misc:511 2011-10-03 21:19:36,238: Started FTP server [INFO] galaxy:113 2011-10-03 21:19:36,238: Starting Galaxy... [DEBUG] misc:511 2011-10-03 21:19:43,828: Successfully initiated Galaxy start. [DEBUG] galaxy:139 2011-10-03 21:19:43,852: Galaxy UI does not seem to be accessible. [DEBUG] ec2:207 2011-10-03 21:19:43,852: Getting boto S3 connection [INFO] misc:394 2011-10-03 21:19:44,143: Saved file 'persistent_data.yaml' to bucket 'cm-6d20503431d38fb901ad6a550b90e0d4' [DEBUG] master:1462 2011-10-03 21:19:44,195: Instance post start script (/mnt/cm/post_start_script) does not exist? [DEBUG] galaxy:139 2011-10-03 21:19:48,544: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:19:48,545: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:04,821: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:04,822: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:21,089: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:21,089: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] galaxy:139 2011-10-03 21:20:37,369: Galaxy UI does not seem to be accessible. [DEBUG] master:1510 2011-10-03 21:20:37,370: S&S: SGE..Starting; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting;

2 1

applications not installed?
by Sofia Robb 04 Oct '11

04 Oct '11

I have installed the local galaxy distribution on my MacBook Pro Mac OS X Version 10.7.1 using hg as described on get galaxy.org hg clone https://bitbucket.org/galaxy/galaxy-dist/ the run.sh script runs, and i am able to open localhost:8080 and i am able to upload data files. I have not tested many applications but it seems that the applications are not installed, or at least bwa and bowtie are not installed from the error I receive. An error occurred running this job: Error indexing reference sequence /bin/sh: bowtie-build: command not found -and- An error occurred running this job: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found Are the applications not installed? I searched for them but could not find them within /galaxy-dist (find /galaxy-dist -name "*bwa*" ). I find wrappers but no apps. Where should they be located? Thanks, Sofia

2 1

iRODS integration
by James Vincent 04 Oct '11

04 Oct '11

Hello, I've read about a number of side projects that integrate iRODS or other file handling things into Galaxy. What are the chances Galaxy could be made to use iRODS as it's primary file store? Instead of storing all files in some local space on a machine, Galaxy would call and act upon iRODS objects. I can think of many, many benefits of such a system, but is there any chance? Jim

2 1

(Composite) Dataset Upload not Setting Metadata
by Paniagua, Eric 04 Oct '11

04 Oct '11

Hi everyone, I've been getting my feet wet with Galaxy development working to get some of the rexpression tools online, and I've run into a snag that I've traced back to a set_meta datatype method not being able to find a file from which it wants to extract metadata. After reading the code, I believe this would also be a problem for non-composite datatypes. The specific test case I've been looking at is uploading an affybatch file (and associated pheno file) using Galaxy's built-in upload tool and selecting the File Format manually (ie choosing "affybatch" in the dropdown). I am using unmodified datatype definitions provided in lib/galaxy/datatypes/genetics.py and unmodified core Galaxy upload code as of 5955:949e4f5fa03a. (I am also testing with modified versions, but I am able to reproduce and track this bug in the specified clean version). The crux of the cause of error is that in JobWrapper.finish(), dataset.set_meta() is called (lib/galaxy/jobs/__init__.py:607) before the composite dataset uploaded files are moved (in a call to a Tool method "self.tool.collect_associated_files(out_data, self.working_directory)" on line 670) from the job working directory to the final destination under config.file_path (which defaults to "database/files"). In my test case, "database.set_meta( overwrite = False )" eventually calls lib/galaxy/datatypes/genetics.py:Rexp.set_meta(dataset, **kwd). As far as I can tell, the only ways to construct a path to a file (or the file) in a dataset without using hard-coded paths from external knowledge is to use the Dataset.get_file_name or Dataset.extra_files_path properties. Unless explicitly told otherwise, both of these methods construct a path based on the Dataset.file_path class data member, whose value is set during Galaxy startup to config.file_path (default "database/files"). However, at the time set_meta is called in this case, the files are not under config.file_path, but rather under the job working directory. Attempting to open files from the dataset therefore fails when using these paths. However, unless the job working directory is passed to set_meta or during construction of the underlying Dataset object, there doesn't appear to be a way for a Dataset method to access the currently running job (for instance to get its job ID or working directory). (The second suggestion is actually not possible; since the standard upload is asynchronous, the Dataset object is created (and persisted) before the Job that will process it is created.) Thoughts? This issue affects Rexp.set_peek also, as well as any other functions that may want to read data from the uploaded files before they are moved to permanent location. This is why if you have an affybatch file and its associated pheno file and you test this on, say, the public Galaxy server at http://main.g2.bx.psu.edu/ you'll see that the peek info says (for example): "##failed to find /galaxy/main_database/files/002/948/dataset_2948818_files/affybatch_test.pheno" It seems that if the current way that Dataset.file_path, Dataset.file_name, and Dataset.extra_files_path is part of the desired design of Galaxy, that methods like set_meta should be run after the files have been moved to config.file_path so they can set metadata based on file contents. It looks like this is intended to happen at least in some cases, from looking at lib/galaxy/jobs/__init__.py:568-586. However, in my tests this code is not kicking in because hda_tool_output is None. Any clarification on what's happening here, what's supposed to be happening for setting metadata on (potentially composite) uploads, why dataset.set_meta() isn't already being called after the files are moved to config.file_path, or any insights on related Galaxy design decisions I may not know about or design constraints I may have missed would be very greatly appreciated. I'd also be glad to provide further detail or test files upon request. Thank you, Eric Paniagua PS: Further notes on passing the job working directory to set_meta or set_peek - I have been successful modifying the code to do this for set_meta since the call chain starting from dataset.set_meta() in JobWrapper.finish() to Rexp.set_meta() accepts and forwards keyword argument dictionaries along the way. However, set_peek does not accept arbitrary keyword arguments, making it harder to pass along the job working directory when needed without stepping on the toes of any other code.

3 12

BWA built-in indexes in Galaxy
by Bruno Zeitouni 04 Oct '11

04 Oct '11

Dear all, I would like to use our built-in color-spaces indexes for BWA with Galaxy but I failed to do it. I added the following line in the "bwa_index_color.loc" file of the "tool-data" directory : hg19 hg19 hg19 my_path_to/hg19.fa but I don't see the reference hg19 appeared onto the browser... ("Map with BWA for SOLiD") Maybe I missed something here because there is a note about the original path for hg19 for workflow backwards compatibility (?), but I don't understand what it means.. For the BFAST indexes, It is OK. Thank you for your help Bruno -- Bruno Zeitouni, PhD Institut Curie - U900 INSERM - Mines ParisTech Equipe Bioinformatique Bâtiment de Biologie du Développement 26 rue d'ULM 75248 Paris Cedex 05 - FRANCE Tél : +33 1 56 24 69 31 Mail : bruno.zeitouni(a)curie.fr

2 1

FW: Galaxy tool error report from khaden@illumina.com
by Haden, Kirt 03 Oct '11

03 Oct '11

Galaxy team, I am running a locally configured Galaxy instance using Python 2.7. I am getting an error on SAM_to_BAM unable to fetch eggs. When I change back to Python 2.6, the problem is removed and I can run the tool. Is there a quick fix for this problem? Thanks, Kirt -----Original Message----- From: khaden(a)illumina.com [mailto:khaden@illumina.com] Sent: Thursday, September 29, 2011 8:07 AM To: Haden, Kirt; Haden, Kirt Subject: Galaxy tool error report from khaden(a)illumina.com GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "ussd-dev-lnx01.illumina.com" ----------------------------------------------------------------------------- This is in reference to dataset id 301 from history id 68 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 7: SAM-to-BAM on data 6: converted BAM by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. ussd-dev-lnx01.illumina.com/history/view?id=42e99d98e0ee2844 ----------------------------------------------------------------------------- The user 'khaden(a)illumina.com' provided the following information: ----------------------------------------------------------------------------- job id: 200 tool id: sam_to_bam ----------------------------------------------------------------------------- job command line: python /home/galaxy/eval/sept09/galaxy-central/tools/samtools/sam_to_bam.py --input1=/home/galaxy/production/Sept06/galaxy-central/database/files/000/dataset_300.dat --dbkey=PhiX --output1=/home/galaxy/production/Sept06/galaxy-central/database/files/000/dataset_301.dat --index_dir=/home/galaxy/eval/sept09/galaxy-central/tool-data ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/home/galaxy/eval/sept09/galaxy-central/tools/samtools/sam_to_bam.py", line 14, in ? import pkg_resources; pkg_resources.require( "bx-python" ) File "/home/galaxy/eval/sept09/galaxy-central/lib/galaxy/eggs/__init__.py", line 415, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['bx_python'] ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

3 2

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
by Nate Coraor 03 Oct '11

03 Oct '11

Sergei Ryazansky wrote: > Hello all, > > we have the UCSC genome browser mirror as well as Galaxy mirror. The > Galaxy has a feature enabling a user to display the data at UCSC genome > browser as custom tracks. I have configured the galaxy to display the data > to our UCSC browser mirror but it doesn't work properly: after the > redirecting to genome browser page the "redirected to non-http(s): /root" > error message is appeared. At the same time displaying Galaxy data at > official UCSC works excellent. What are the possible reasons of it? > Thank you in advance! Hi Sergei, If your Galaxy server is behind a proxy server serving via https, have you set the following header: RequestHeader set X-URL-SCHEME https Please see the "SSL" section of the ApacheProxy page for more information: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy --nate > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

4 7

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galaxy-dev October 2011