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first install, MySQL date
by Arnau Bria 01 Mar '13

01 Mar '13

Hi all, my name is Arnau Bria and I work at CRG, in BCN. I'm a sysadmin and I'm helping one user to install/configure galaxy and to run jobs in our SGE cluster. I think this is the correct list for asking SGE/MySQL questions, if not, let me apology in advance. I have a question about MySQL dates. system date is correct and uses CET (I'm in Spain), MySQL i sconfigured to use system's timezone: date Thu Feb 28 13:38:10 CET 2013 SELECT @@global.time_zone, @@session.time_zone; +--------------------+---------------------+ | @@global.time_zone | @@session.time_zone | +--------------------+---------------------+ | SYSTEM | SYSTEM | +--------------------+---------------------+ 1 row in set (0.02 sec) but SGE job dates are wrong: create_time 2013-02-28 12:37:48 notice it shows 12:37 and it should be 13:37. is this importatn? may I change glaxy's timezone in some way? TIA, Arnau

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Error while installing DESeq-hts
by Philipe Moncuquet 01 Mar '13

01 Mar '13

Hi, I have tried to follow instructions provided with this installation a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts. I successfully ran the setup scrip but is there other path and conf that need to be done apart from those done by this script ? b) Inside the mex folder execute the make file to create platform dependent .mex files cd mex/Makefile make [interpreter] make octave for octave make matlab for matlab make all for octave and matlab When I run make octave I get the following error message : /usr/bin/mkoctfile -g --mex get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I/mnt/galaxyTools/tools/samtools/0.1.16 -L/mnt/galaxyTools/tools/samtools/0.1.16 -lbam -lz -lcurses get_reads_direct.cpp:14:17: fatal error: sam.h: No such file or directory compilation terminated. make: *** [get_reads.mex] Error 1 It feels like this is link to samtools, when browsing on the web I found information about SAMTOOLS_ROOT env variable but changing this one doesn't solve my problem. As anyone else encounter this kind of things ? Regards, Philippe

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March 2013 Galaxy Update
by Dave Clements 01 Mar '13

01 Mar '13

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Error on the sandbox toolshed when updating files
by Peter Waltman 01 Mar '13

01 Mar '13

Hi - I was only trying to upload a new gzipped-tarfile with new files to a repository that I own on the sandbox toolshed server, and get the following error: Server ErrorURL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d… Module paste.exceptions.errormiddleware:*144* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*128* in __call__ >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*184* in handle_request >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*94* in decorator >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.tool_shed.controllers.upload:*108* in upload >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> self*.*upload_tar*(* trans*,* repository*,* tar*,* uploaded_file*,* upload_point*,* remove_repo_files_not_in_tar*,* commit_message*,* new_repo_alert *)* Module galaxy.webapps.tool_shed.controllers.upload:*283* in upload_tar >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> *return* self*.*__handle_directory_changes*(*trans*,* repository*,* full_path*,* filenames_in_archive*,* remove_repo_files_not_in_tar*,* new_repo_alert*,* commit_message*,* undesirable_dirs_removed*,* undesirable_files_removed*)* Module galaxy.webapps.tool_shed.controllers.upload:*345* in __handle_directory_changes >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> commands*.*commit*(* repo*.*ui*,* repo*,* full_path*,* user*=*trans*.*user*. *username*,* message*=*commit_message *)* Module mercurial.commands:*1279* in commit >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> node *=* cmdutil*.*commit*(*ui*,* repo*,* commitfunc*,* pats*,* opts*)* Module mercurial.cmdutil:*1294* in commit >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> scmutil*.*match*(*repo*[*None*]**,* pats*,* opts*)**,* opts*)* Module mercurial.commands:*1277* in commitfunc >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> match*,* editor*=*e*,* extra*=*extra*)* Module mercurial.localrepo:*1199* in commit >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> ret *=* self*.*commitctx*(*cctx*,* True*)* Module mercurial.localrepo:*1270* in commitctx >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> p2*.*manifestnode*(**)**,* *(*new*,* drop*)**)* Module mercurial.manifest:*197* in add >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> cachedelta *=* *(*self*.*rev*(*p1*)**,* addlistdelta*(*addlist*,* delta*)**) * Module mercurial.manifest:*124* in addlistdelta >> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d…> addlist*[*start*:*end*]* *=* array*.*array*(*'c'*,* content*)* *TypeError: array item must be char* Is there a better way to upload updated files to those repositories? -- Peter Waltman, Ph.D. pwaltman(a)ucsc.edu 617.347.187

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Coming soon: BOSC/Broad Hackathon, SciPy Bioinformatics, BOSC Codefest
by Brad Chapman 01 Mar '13

01 Mar '13

Hi all; There are some upcoming coding events and conferences of interest to open source biology programmers: - BOSC/Broad Interoperability Hackathon -- This is a two day coding session at the Broad Institute in Cambridge, MA on April 7-8 focused on improving tool interoperability. Sign up and details: http://j.mp/XJT6ew - SciPy 2013 -- The Scientific Python conference is June 26-27 in Austin and has a Bioinformatics mini-symposia this year. They're doing some great work like IPython, NumPy, SciPy and scikit-learn; and this is a nice opportunity to reach a new set of like minded programmers and expand the open source bioinformatics community. Bioinformatics mini-symposia: http://j.mp/Z4xxXB Abstract details: http://conference.scipy.org/scipy2013/about.php - Codefest at the Bioinformatics Open Source Conference -- This year BOSC is taking place in Berlin from July 19-20 and we'll have a two day coding session before the conference. This is the 4th year of Codefests and they've proven to be a productive and fun time to work collectively on open source projects. Sign up and details: http://www.open-bio.org/wiki/Codefest_2013 BOSC conference: http://www.open-bio.org/wiki/BOSC_2013 Here are the key dates for the events and abstracts: March 20, 2013: SciPy abstracts due April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA April 12, 2013: BOSC abstracts due June 24-29, 2013: SciPy in Austin, TX July 17-18, 2013: Codefest 2013, Berlin July 19-20, 2013: BOSC 2013, Berlin Looking forward to seeing everyone this spring and summer for plenty of fun science and code, Brad

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cleanup script fails on dataset_instance "None"
by Anthonius deBoer 01 Mar '13

01 Mar '13

Hi, I have some problems with the cleanup scripts... I seem to have a dataset_instance that is "None" and if it tries to delete that you obviously get an error. (See below..>I added the print statement, but the line is the same)... I wonder how I could get a dataset with a None definition and how can I clean up the database for this? Thanks, Thon sh < purge_libraries.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 527, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 122, in main purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 217, in purge_libraries _purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 498, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance print('dataset_instance.id: {0}'.format(dataset_instance.id)) AttributeError: 'NoneType' object has no attribute 'id' (galaxy_env)[svcgalaxy@srv151 cleanup_datasets]$ sh < purge_libraries.sh

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bowtie-wrapper
by Alexander Kurze 01 Mar '13

01 Mar '13

Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output: > bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s) The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341

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purging datasets doesn't free up disk space
by Sarah Diehl 28 Feb '13

28 Feb '13

Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah

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access to api when using apache ldap auth
by Langhorst, Brad 28 Feb '13

28 Feb '13

I need to access the api using an api key… Does anybody have a working apache configuration for that? A search at galaxyproject.org/search<http://galaxyproject.org/search> didn't turn anything up. I tried this: but that causes the history to fail to update. <Location "/"> Order allow,deny allow from all AuthType Basic AuthName "NEB Credentials" AuthBasicProvider ldap AuthzLDAPAuthoritative off AuthLDAPBindDN xxxx@yyyy AuthLDAPBindPassword xxxxx AuthLDAPURL "ldap://<host…>?sAMAccountName" require valid-user RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary XSendFile on XSendFileAllowAbove on </Location> <Location "/api"> Satisfy Any Allow from all </Location> I must keep that /api location commented out for history updates to work. If i uncomment it, i can use the api. What's the right solution? Maybe i should add a /api2 alias that does not require valid-user? Maybe my apache foo is just too weak and I'm missing something obvious? Thanks for any advice! Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Macs14 - Invalid Literal for int error
by greg 28 Feb '13

28 Feb '13

Hi guys, (Sorry for showing up on this list so much, hopefully I'll get everything running soon!) On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg we get this error: Dataset generation errors Dataset 74: MACS14 on data 29 and data 24 (peaks: bed) Tool execution generated the following error message: Traceback (most recent call last): File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 132, in <module> if __name__ == "__main__": main() File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py", line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start'

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