- galaxy-dev - lists.galaxyproject.org

Issue, displaying or downloading data.
by michael burrell (TOC) 18 Oct '11

18 Oct '11

Good Morning, I have had the following issue reported to me by one of our users and I have confirmed the behaviour. Hi Mike, I'm looking at the new Galaxy at http://jic55666:8080/root and I have found a problem. If I import a dataset from the data libraries, then stuff runs OK. If I upload a dataset from a file I get the following problems. 1. I can view data preview in history item, but can't view data in main panel (by clicking on the eye) 2. Tools run on file-uploaded data execute OK and appear to produce output (again viewable in history item), but data can't be viewed in main panel. 3. Downloading any datasets created from file-uploaded dataset, result in an empty file. 4. If I upload a file to Galaxy and then save it back to disk, it's empty. Some further specifics on our install galaxy@jic55666:~/software/galaxy-central$ hg tip changeset: 6042:2469c53051ea tag: tip user: Daniel Blankenberg <dan(a)bx.psu.edu> date: Sun Sep 25 13:27:14 2011 -0400 summary: Some random lines tool tweaks. Thanks Michael. ----------------------------------------------------------------------------------------------------- Please note, that my email address is no longer givenname.surname(a)bbsrc.ac.uk. Please update your records to reflect my new email address of givenname.surname(a)nbi.ac.uk as shown on this email.

2 1

Admin Delete Users
by lentaing＠jimmy.harvard.edu 18 Oct '11

18 Oct '11

Hi, I noticed on that on the manage users page, even after deleting and purging users (by clicking on the delete and purge buttons on that page), their account still sticks around in the db. How does one remove these accounts permanently? Is there a script to do this? Thanks, Len

2 1

galaxy cloud install hangs
by Joseph Hargitai 18 Oct '11

18 Oct '11

Hi, trying to bring up a new instance. 1, remove old cm from S3 bucket 2, bring up new 3, get console 4, SGE and fs running 5,Database and galaxy are not running 6, on /mnt i see /mnt and galaxyData East 1c xy Cloudman Admin | Report bugs | Wiki | Screencast Only up to the most recent 200 lines of the file (paster.log) are shown. Show all | Show less | Show more | Back to admin view [DEBUG] sge:311 2011-10-14 08:54:00,368: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.24 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:54:00,445: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:54:16,706: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.24 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:54:16,759: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:54:33,018: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.24 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:54:33,085: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:54:49,421: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:54:49,853: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:06,110: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:55:06,161: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:22,440: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:55:22,754: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:39,011: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:55:39,063: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:55,326: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:55:55,375: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:56:11,634: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:56:11,684: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:56:27,948: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:56:28,002: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:56:44,264: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:56:44,356: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:00,623: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:57:00,672: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:16,920: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.17 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:57:16,971: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:33,229: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.17 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:57:33,276: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:49,529: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.17 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:57:49,579: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:05,844: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.18 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:58:05,938: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:22,207: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.18 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:58:22,258: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:38,512: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.14 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:58:38,562: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:54,832: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.14 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:58:54,896: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:59:11,159: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.14 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:59:11,223: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:59:27,542: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.09 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:59:27,631: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:59:43,920: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.09 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 08:59:43,968: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:00:00,232: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.06 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:00:00,285: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:00:16,552: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.06 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:00:16,636: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] master:468 2011-10-14 09:00:17,717: List of services before shutdown: ['SGE', 'FS-galaxyData'] [DEBUG] master:237 2011-10-14 09:00:17,718: Not stopping autoscaling because it is not on. [INFO] sge:28 2011-10-14 09:00:17,718: Removing SGE service [DEBUG] misc:511 2011-10-14 09:00:17,945: Successfully stopped SGE master [INFO] master:498 2011-10-14 09:00:17,946: Cluster shut down at 2011-10-14 09:00:17.946341 (uptime: 6:16:36.067737). If not done automatically, manually terminate the master instance (and any remaining instances associated with this cluster) from the AWS console. Python version: (2, 6) [DEBUG] app:42 2011-10-14 09:01:05,719: Initializing app [DEBUG] ec2:207 2011-10-14 09:01:05,719: Getting boto S3 connection [DEBUG] ec2:209 2011-10-14 09:01:05,719: No S3 Connection, creating a new one. [DEBUG] ec2:212 2011-10-14 09:01:05,719: Got boto S3 connection. [INFO] misc:378 2011-10-14 09:01:05,792: Retrieved file 'persistent_data.yaml' from bucket 'cm-cefdad8733f8efe0be7f3c3f5059d9b8' to 'pd.yaml'. [INFO] app:52 2011-10-14 09:01:05,794: Master starting [DEBUG] master:50 2011-10-14 09:01:05,826: Initializing console manager - cluster start time: 2011-10-14 09:01:05.826253 [DEBUG] connection:648 2011-10-14 09:01:05,828: 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 2011-10-14 09:01:05,865: Open OK! known_hosts [ip-10-191-205-72.ec2.internal:5672] [DEBUG] channel:70 2011-10-14 09:01:05,865: using channel_id: 1 [DEBUG] channel:484 2011-10-14 09:01:05,866: Channel open [DEBUG] comm:35 2011-10-14 09:01:05,867: Successfully established AMQP connection [DEBUG] master:436 2011-10-14 09:01:05,867: Trying to discover any worker instances associated with this cluster... [DEBUG] ec2:177 2011-10-14 09:01:05,867: Establishing boto EC2 connection [DEBUG] ec2:85 2011-10-14 09:01:05,868: Gathering instance zone, attempt 0 [DEBUG] ec2:90 2011-10-14 09:01:05,870: Instance zone is 'us-east-1c' [DEBUG] ec2:198 2011-10-14 09:01:06,078: Got boto EC2 connection for region 'us-east-1' [DEBUG] ec2:66 2011-10-14 09:01:06,128: Gathering instance id, attempt 0 [DEBUG] ec2:71 2011-10-14 09:01:06,130: Instance ID is 'i-2e4f734e' [DEBUG] ec2:228 2011-10-14 09:01:06,215: Adding tag 'clusterName:WASP' to resource 'i-2e4f734e' [DEBUG] ec2:228 2011-10-14 09:01:06,257: Adding tag 'role:master' to resource 'i-2e4f734e' [DEBUG] master:147 2011-10-14 09:01:06,299: ud at manager start: {'access_key': 'AKIAI4G3E4I2722APZZA', 'data_filesystems': {'galaxyData': [{'vol_id': 'vol-872314ed', 'size': 700}]}, 'cloudman_home': '/mnt/cm', 'cluster_name': 'WASP', 'services': [{'service': 'SGE'}], 'bucket_default': 'cloudman', 'boot_script_name': 'cm_boot.py', 'bucket_cluster': 'cm-cefdad8733f8efe0be7f3c3f5059d9b8', 'boot_script_path': '/tmp/cm', 'role': 'master', 'secret_key': 'ygWVriMaS0osJC6Ix3QZvKue19EdLtL5yUV7EuAY', 'password': 'WASP'} [DEBUG] master:455 2011-10-14 09:01:06,299: Trying to discover any volumes attached to this instance... [DEBUG] base:55 2011-10-14 09:01:06,303: Enabling 'root' controller, class: CM [DEBUG] buildapp:80 2011-10-14 09:01:06,305: Enabling 'httpexceptions' middleware [DEBUG] buildapp:86 2011-10-14 09:01:06,307: Enabling 'recursive' middleware [DEBUG] buildapp:106 2011-10-14 09:01:06,320: Enabling 'print debug' middleware [DEBUG] buildapp:120 2011-10-14 09:01:06,338: Enabling 'error' middleware [DEBUG] buildapp:130 2011-10-14 09:01:06,338: Enabling 'config' middleware [DEBUG] buildapp:134 2011-10-14 09:01:06,339: Enabling 'x-forwarded-host' middleware Starting server in PID 1009. [DEBUG] master:461 2011-10-14 09:01:06,369: Attached volumes: [Volume:vol-1b251271, Volume:vol-872314ed] [DEBUG] master:185 2011-10-14 09:01:06,369: Adding a previously existing data filesystem: 'galaxyData' [DEBUG] master:193 2011-10-14 09:01:06,369: Adding service: 'SGE' [INFO] master:155 2011-10-14 09:01:06,369: Completed initial cluster configuration. [DEBUG] master:1488 2011-10-14 09:01:06,369: Monitor started; manager started serving on 0.0.0.0:42284 view at http://127.0.0.1:42284 [DEBUG] master:1515 2011-10-14 09:01:10,372: Monitor adding service 'SGE' [DEBUG] __init__:31 2011-10-14 09:01:10,372: Trying to add service 'SGE' [INFO] __init__:49 2011-10-14 09:01:10,372: Prerequisites OK; starting service 'SGE' [DEBUG] sge:61 2011-10-14 09:01:10,372: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] __init__:42 2011-10-14 09:01:10,434: 'sge' daemon is NOT running any more (expected pid: '2530'). [DEBUG] sge:76 2011-10-14 09:01:10,435: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-10-14 09:01:10,934: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-10-14 09:01:12,949: Configuring SGE... [DEBUG] ec2:136 2011-10-14 09:01:12,949: Gathering instance private hostname, attempt 0 [DEBUG] sge:104 2011-10-14 09:01:12,952: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-10-14 09:01:12,952: Setting up SGE. [DEBUG] misc:511 2011-10-14 09:01:20,181: Successfully set up SGE [INFO] sge:114 2011-10-14 09:01:20,181: Successfully setup SGE; configuring SGE [DEBUG] sge:119 2011-10-14 09:01:20,182: Created SGE all.q template as file '/opt/sge/all.q.conf' [DEBUG] misc:511 2011-10-14 09:01:20,200: Successfully modified all.q [DEBUG] misc:511 2011-10-14 09:01:20,211: Modified /opt/sge/util/arch [DEBUG] misc:511 2011-10-14 09:01:20,217: Successfully chmod /opt/sge/util/arch [DEBUG] sge:125 2011-10-14 09:01:20,218: Configuring users' SGE profiles [DEBUG] master:1515 2011-10-14 09:01:20,220: Monitor adding service 'FS-galaxyData' [DEBUG] filesystem:311 2011-10-14 09:01:20,220: Trying to add service 'FS-galaxyData' [DEBUG] filesystem:143 2011-10-14 09:01:20,397: Tried to create a volume but it is in state 'attached' (volume ID: vol-872314ed) [DEBUG] ec2:228 2011-10-14 09:01:20,397: Adding tag 'clusterName:WASP' to resource 'vol-872314ed' [DEBUG] ec2:228 2011-10-14 09:01:20,435: Adding tag 'filesystem:galaxyData' to resource 'vol-872314ed' [DEBUG] filesystem:214 2011-10-14 09:01:20,641: Tried to attach a volume but the volume 'vol-872314ed' is already attached (as device /dev/sdg1) [DEBUG] filesystem:426 2011-10-14 09:01:20,726: Path '/dev/sdg1' checked and exists. [DEBUG] misc:511 2011-10-14 09:01:20,862: Successfully mounted file system '/mnt/galaxyData' from '/dev/sdg1' [DEBUG] misc:511 2011-10-14 09:01:20,874: Successfully edited '/mnt/galaxyData' in '/etc/exports' for NFS. [DEBUG] misc:511 2011-10-14 09:01:21,962: As part of filesystem 'Filesystem-galaxyData' update, successfully restarted NFS server [DEBUG] ec2:207 2011-10-14 09:01:22,014: Getting boto S3 connection [INFO] misc:394 2011-10-14 09:01:22,109: Saved file 'persistent_data.yaml' to bucket 'cm-cefdad8733f8efe0be7f3c3f5059d9b8' [DEBUG] master:1462 2011-10-14 09:01:22,139: Instance post start script (/mnt/cm/post_start_script) does not exist? [DEBUG] sge:311 2011-10-14 09:01:26,429: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.08 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:01:26,485: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:01:42,730: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.08 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:01:42,785: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:01:59,035: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.08 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:01:59,089: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:02:15,330: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.24 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:02:15,407: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:02:31,656: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.24 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:02:31,706: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:02:47,950: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.36 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:02:48,002: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:03:04,261: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.36 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:03:04,312: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:03:20,568: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.36 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:03:20,614: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:03:36,870: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.44 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:03:36,914: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:03:53,167: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.44 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:03:53,252: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:04:09,499: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.59 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:04:09,550: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:04:25,800: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.59 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:04:25,847: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:04:42,094: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.68 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:04:42,150: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:04:58,405: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.68 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:04:58,482: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:05:14,736: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.68 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:05:14,784: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:05:31,037: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.76 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:05:31,087: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:05:47,336: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.76 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:05:47,383: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:06:03,697: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.87 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:06:03,748: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:06:19,994: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.87 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:06:20,045: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:06:36,297: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 0.87 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:06:36,369: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:06:52,621: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:06:52,677: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:07:08,931: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:07:08,982: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:07:25,231: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:07:25,286: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:07:41,534: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:07:41,617: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:07:57,865: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:07:57,911: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:08:14,164: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.01 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:08:14,211: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:08:30,453: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.01 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:08:30,499: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:08:46,746: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.06 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:08:46,796: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:09:03,051: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.06 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:09:03,107: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:09:19,360: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.06 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:09:19,442: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:09:35,698: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:09:35,751: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:09:52,063: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.00 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:09:52,106: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:10:08,360: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.05 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:10:08,419: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:10:24,674: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.05 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:10:24,754: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:10:40,999: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.05 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:10:41,046: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:10:57,295: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.05 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:10:57,344: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:11:13,595: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.05 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:11:13,646: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:11:29,895: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.03 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:11:29,947: S&S: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 09:11:46,190: qstat: ['all.q(a)ip-10-191-205-72.ec2.int BIP 0/0/4 1.03 lx24-amd64 '] [DEBUG] master:1510 2011-10-14 09:11:46,234: S&S: SGE..OK; FS-galaxyData..OK;

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Re: [galaxy-dev] Hi Galaxy
by meshashi29＠gmail.com 17 Oct '11

17 Oct '11

Hey Galaxy we haven't spoken in a while. Are you interested in making any money? http://t.co/sJs9hfhx Read this newspaper page! I have made so much money using this program.

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Re: [galaxy-dev] Hello
by meshashi29＠gmail.com 17 Oct '11

17 Oct '11

hope you're doing well. Are you interested in making some money? http://t.co/Q8clVaMu Just check out this news article! I thank God that I found this opportunity and for my success!

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(i18n) How to make Galaxy display in Japanese?
by 孙翰菲 17 Oct '11

17 Oct '11

Hi,all I'm trying to translate galaxy into Chinese recently. I found there's a directory "locale" under the galaxy directory, it looks like this: . |-- en | `-- LC_MESSAGES | |-- ginga.mo | |-- ginga.po | |-- tools.mo | `-- tools.po |-- ginga.pot |-- ja | `-- LC_MESSAGES | |-- ginga.mo | |-- ginga.po | |-- tools.mo | `-- tools.po |-- tools.pot It seems that Galaxy could display in Japanese, then I stopped the running galaxy service on the localhost and tried: # export LANG=ja_JP.utf-8 # run.sh But the webpage is still English. Then I copied the *.mo files to /usr/share/locale/ja_JP/LC_MESSAGES, but it doesn't work either. Does anyone know whether it's possible to display galaxy in Japanese now? Thanks! HF

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GALAXY_URL with port 8080
by Joseph Hargitai 16 Oct '11

16 Oct '11

Hi, just noticed that in our current setup the baseurl to post data back from ucsc tablebrowser is not picking up the port designation. I looked at two files: ucsc_display_sites <inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> <display>go to UCSC Table Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> <param name="tool_id" type="hidden" value="ucsc_table_direct_test1" /> <param name="sendToGalaxy" type="hidden" value="1" /> <param name="hgta_compressType" type="hidden" value="none" /> <param name="hgta_outputType" type="hidden" value="bed" /> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> it looks like too late to modify this part. and in __init__.py can somewhere the GALAXY_URL or REDIRECT_URL to reflect http:/site.blah.edu:8000/galaxy versus what it does now http:/site.blah.edu/galaxy ? Where/home __init__.py picking up the wrong url here? If it is from the *.ini setting of cookie path and cookie - can that be set to :8080/galaxy ? thanks, joe

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MAF tools issues on Galaxy
by Marcin Jakalski 15 Oct '11

15 Oct '11

Hi, I want to share a few issues on the performance of tools for working with MAF alignments in the "Fetch Alignments" section in Galaxy. *The first issue* I have is with the "Stitch MAF blocks given a set of genomic intervals" tool. For a given set of genomic intervals I use this tool to obtain, in my case, the human and the corresponding mouse sequences from 17-way MULTIZ alignment. The problem is, that in the case of insertions in the mouse sequence, the human sequence, which is a reference (the intervals are for human genome) does not contain any gaps. The gaps are only present in mouse sequence. So when there is any insertion in mouse, there are no gaps in the human sequence - simply this portion of alignment is not fetched. *The second issue*. It is somehow related to the first issue. To overcome the problem described above I used the "Extract MAF blocks given a set of genomic intervals" tool. Here I get a set of MAF block that overlap my intervals, and because one set of intervals can overlap with more than one block, the number of resulting block is of course higher than the initial number of intervals. Now I can use the "Join MAF blocks by Species" tool to join some of this smaller block to get the full overlap of my intervals. However, this tool is sensitive on the order of MAF blocks, meaning the blocks that look like the ones below will be joined to one block with 28nt in length, but if we reverse their order, they won't be joined together. s hg18.chr10 101141372 14 + 135374737 CTGCCTTCCCTTCC s mm8.chr19 43548455 10 + 61321190 CGGCCCTTCA---- s hg18.chr10 101141386 14 + 135374737 ATCTCTTCACCCCT s mm8.chr19 43548465 12 + 61321190 --CCCTTCACCCCT This is also specific to the strand, so for the '+' and the '-' strand the order of blocks has to be different, meaning, ascending for the '+', and descending for the '-' strand. *The third issue* is with the "Reverse Complement a MAF file" tool. The reverse complement sequence that I get is actually good, there's nothing wrong with it, but the problem is, that the coordinates change, meaning, tool starts counting from the end position of a chromosome, not from the start position. So now if I want to relate my genomic intervals with the resulting MAF block which I reverse-complemented no I can't do this, because coordinates changed for the second one. So to do that I need to take the length of chromosome and subtract the start position from it, then subtract length and only then I get the same coordinate as in my set of intervals. I think it would be better if the tool would keep the original coordinates. Marcin

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moving the galaxy-dist folder structure
by Joseph Hargitai 14 Oct '11

14 Oct '11

Hi, we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like fastqc, stopped working. Are there internal links that we possibly ignored? Is there a way to adjust the installation via a download or update? joe

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Re: [galaxy-dev] [galaxy-user] Problem with new tool shed
by Greg Von Kuster 14 Oct '11

14 Oct '11

Hello Florent, Sorry for the confusion on this - we are preparing a new Galaxy distribution, and the tool shed wiki has been written in preparation for it. The new distribution will be available fairly soon, and the Galaxy News Brief will include information about these new tool shed features. In any case, you have already discovered that you can use in if you update your Galaxy instance to the latest Galaxy development repository ( Galaxy central ). The problem you see is most likely caused by your not having configured an additional tool_config_file setting in your universe_wsgi.ini. Look for something like following in your latest version of the universe_wsgi.ini.sample that you got when you updated from Galaxy central. # Locally installed tools and tools installed from tool sheds tool_config_file = tool_conf.xml,shed_tool_conf.xml If you add a new additional file name like shed_tool_conf.xml, you should not have a problem installing from a tool shed. I'll have a fix for the bug you've discovered shortly, but making this change will fix the behavior until then. Let me know if you bump into any additional problems. Thanks for finding this! Greg Von Kuster On Oct 4, 2011, at 2:53 AM, Florent Angly wrote: > Hi all, > > I tried the latest stable version of Galaxy: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how to use the new tool shed including how to automatically deploy tools from the shed in a local Galaxy server. > The documentation mentioned some tool shed options available from the the admin section of Galaxy but I could not locate these options in my instance of galaxy. So my question is: Can one only take advantage of the tool deployment from the shed in the development version of Galaxy? If so, I think the Tool shed wiki should be more clear about this. > > Then I tried the latest development version of Galaxy and could locate the tool shed deployment options. I attempted to install the Grinder wrapper (http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp… <http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp…>) but ran into an error that I am pasting below: >> URL: http://localhost:8080/admin/install_tool_shed_repository?tool_shed_url=tool… >> File '/home/floflooo_mint/Software/galaxy-central/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond >> app_iter = self.application(environ, detect_start_response) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ >> environ, self.app) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output >> app_iter = application(environ, replacement_start_response) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ >> return self.application(environ, start_response) >> File '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ >> return self.application(environ, start_response) >> File '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ >> body = method( trans, **kwargs ) >> File '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/__init__.py', line 173 in decorator >> return func( self, trans, *args, **kwargs ) >> File '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/controllers/admin.py', line 805 in install_tool_shed_repository >> shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' ) >> IndexError: list index out of range > > I get the same problem with other wrappers such as FastQC. Am I doing something wrong? > > Thanks, > > Florent > > > ___________________________________________________________ > 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/ Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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