January 2013 - galaxy-dev - lists.galaxyproject.org

Error opening galaxy.json file
by Peter Cock 25 Jan '13

25 Jan '13

Hi all, Could someone explain to me what the "Error opening galaxy.json file" logging means (set at DEBUG level so perhaps not really an error). I've seen this when my development Galaxy is running normally (here I have the logging set to show the DEBUG output) but also for the Galaxy unit tests. e.g. galaxy.jobs.manager DEBUG 2013-01-25 10:37:45,645 (2) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-01-25 10:37:50,899 (2) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/2 galaxy.jobs.handler DEBUG 2013-01-25 10:37:50,900 dispatching job 2 to local runner galaxy.jobs.handler INFO 2013-01-25 10:37:51,175 (2) Job dispatched galaxy.jobs.runners.local DEBUG 2013-01-25 10:37:51,286 Local runner: starting job 2 galaxy.jobs.runners.local DEBUG 2013-01-25 10:37:51,820 executing: python /mnt/galaxy/galaxy-central/tools/protein_analysis/tmhmm2.py "$NSLOTS" /tmp/tmp6hm9Td/database/files/000/dataset_1.dat /tmp/tmp6hm9Td/database/files/000/dataset_2.dat galaxy.jobs.runners.local DEBUG 2013-01-25 10:38:11,967 execution finished: python /mnt/galaxy/galaxy-central/tools/protein_analysis/tmhmm2.py "$NSLOTS" /tmp/tmp6hm9Td/database/files/000/dataset_1.dat /tmp/tmp6hm9Td/database/files/000/dataset_2.dat galaxy.tools DEBUG 2013-01-25 10:38:12,265 Error opening galaxy.json file: [Errno 2] No such file or directory: '/mnt/galaxy/galaxy-central/database/job_working_directory/000/2/galaxy.json' galaxy.jobs DEBUG 2013-01-25 10:38:12,411 job 2 ended Thanks, Peter

2 2

Job manager crashes at start of Galaxy
by Joachim Jacob |VIB| 25 Jan '13

25 Jan '13

Hi all, The jobmanager crashes when Galaxy starts. Starting server in PID 28704. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 303, in command serve() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 287, in serve server(app) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 358, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.gaierror: [Errno -2] Name or service not known galaxy.jobs.manager INFO 2013-01-24 14:05:22,524 sending stop signal to worker thread galaxy.jobs.manager INFO 2013-01-24 14:05:22,524 job manager queue stopped galaxy.jobs.manager INFO 2013-01-24 14:05:22,524 sending stop signal to worker thread galaxy.jobs.manager INFO 2013-01-24 14:05:22,524 job manager stop queue stopped Removing PID file manager.pid After searching a bit on that error (socket.gaierror: [Errno -2] Name or service not known), it might be rooted in my fiddling with the hostname (/etc/hosts). However, I cannot seems to resolve it... Any hints? Thanks, Joachim PS: sorry for the repost, but previous message had an inappropriate Subject line -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

1 1

My fix for error during EMBOSS toolshed install
by Kevin Ying 25 Jan '13

25 Jan '13

Hi, I tried posting this using the contact repo owner but it's giving me error turn on debug mode message. I tried installing emboss_5 on ubuntu 12.04 but got an error (from the gui) In file included from clique.c:1:0: ../include/phylip.h:23:20: fatal error: emboss.h: No such file or directory compilation terminated. make[1]: *** [clique.o] Error 1 make: *** [all-recursive] Error 1 Compiling on the command line by hand using commands in tool dep xml showed issues with X* libraries. In shed_tools/....../tool_dependencies.xml I changed the --without-x line to --without-X and the tool installed fine Kevin.

1 0

BED files not recognized correctly
by Anthonius deBoer 24 Jan '13

24 Jan '13

Hi, I have noticed for a while now that BED files are not recognized correctly or at least not parsed out correctly. I notice that invariably, the (9 column) BED file comments state there is 1 region and X comments, where X + 1 is the actual number of regions in the file.. Here's a few lines from the file 1 38076950 38077349 utr3:RSPO1 1 - 38077349 38077349 0,0,255 1 38077420 38078426 utr3:RSPO1 1 - 38078426 38078426 0,0,255 1 38078426 38078593 cds:RSPO1 1 - 38078426 38078593 255,0,0 1 38079375 38079564 cds:RSPO1 1 - 38079375 38079564 255,0,0 1 38079855 38080005 cds:RSPO1 1 - 38079855 38080005 255,0,0 1 38082155 38082347 cds:RSPO1 1 - 38082155 38082347 255,0,0 1 38095239 38095333 cds:RSPO1 1 - 38095239 38095333 255,0,0 1 38095333 38095621 utr5:RSPO1 1 - 38095621 38095621 0,0,255 Any ideas why it thinks there are comments in the file and why only one region? The file is a regular txt file without the LF and is not DOS format or anything... It also does not parse out the name, score and strand info, but once I correct that manually, it works, but it is a pain to have to do that everytime... Thanks, Thon

3 4

Possible addition of conversion tool bedGraphToBigWig?
by Brian Lee 24 Jan '13

24 Jan '13

Dear Galaxy, Thank you for your excellent resources that enable users to convert formats such as Wig-to-bigWig. Some of UCSC Genome Browser hardware challenged users who operate with a 32-bit system try to convert bedGraph files to BigWig files, however we only compile 64-bit versions. We could not help but wonder if it might bepossible to add to the conversion tool bedGraphToBigWig, http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/, to your excellent list of tools so as to help such users by directing them to your site? All the best, Brian Lee UCSC Genome Bioinformatics Group

3 3

Fw: Error when attempting to install new distributuion - TypeError: Invalid argument(s) 'server_side_cursors', 'max_overflow'
by Liisa Koski 24 Jan '13

24 Jan '13

Hello, I am attempting to install a new galaxy-dist and am running into the following error. I first tried it by using a mysql database but this error also occurs when I use the default SQLite database. Any help would be much appreciated. Thanks in advance, Liisa [galaxy-dev]$ ./run.sh Some eggs are out of date, attempting to fetch... Fetched http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-l… Fetch successful. galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: galaxy-dev/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/boto-2.5.2-py2.6.egg, galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/Fabric-1.4.2-py2.6.egg, galaxy-dev/eggs/ssh-1.7.14-py2.6.egg, galaxy-dev/eggs/Whoosh-0.3.18-py2.6.egg, galaxy-dev/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/amqplib-0.6.1-py2.6.egg, galaxy-dev/eggs/pexpect-2.4-py2.6.egg, galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, galaxy-dev/eggs/Babel-0.9.4-py2.6.egg, galaxy-dev/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/Mako-0.4.1-py2.6.egg, galaxy-dev/eggs/WebHelpers-0.2-py2.6.egg, galaxy-dev/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/wchartype-0.1-py2.6.egg, galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg, galaxy-dev/eggs/docutils-0.7-py2.6.egg, galaxy-dev/eggs/WebOb-0.8.5-py2.6.egg, galaxy-dev/eggs/Routes-1.12.3-py2.6.egg, galaxy-dev/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, galaxy-dev/eggs/PasteDeploy-1.3.3-py2.6.egg, galaxy-dev/eggs/PasteScript-1.7.3-py2.6.egg, galaxy-dev/eggs/Paste-1.6-py2.6.egg, galaxy-dev/lib, /usr/lib64/python2.6/site-packages/distribute-0.6.12-py2.6.egg, /usr/lib64/python2.6/site-packages/blist-1.3.4-py2.6-linux-x86_64.egg, /usr/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg, /usr/lib/python2.6/site-packages/argparse-1.2.1-py2.6.egg, /usr/lib/python2.6/site-packages/pip-1.2.1-py2.6.egg, /usr/lib/python2.6/site-packages, /usr/lib64/python2.6/xml/etree, /usr/lib64/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/PIL, /usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, /usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, /usr/lib64/python2.6/site-packages galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-01-21 13:52:06,112 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): File "galaxy-dev/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "galaxy-dev/lib/galaxy/app.py", line 45, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "galaxy-dev/lib/galaxy/model/migrate/check.py", line 46, in create_or_verify_database engine = create_engine( url, **engine_options ) File "galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/__init__.py", line 223, in create_engine return strategy.create(*args, **kwargs) File "galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py", line 121, in create engineclass.__name__)) TypeError: Invalid argument(s) 'server_side_cursors','max_overflow' sent to create_engine(), using configuration SQLiteDialect/SingletonThreadPool/TLEngine. Please check that the keyword arguments are appropriate for this combination of components.

2 2

Re: [galaxy-dev] igvtools
by Jim Johnson 24 Jan '13

24 Jan '13

Jorge, I think that I omitted the igvtools index command because galaxy implicitly manages indexes for datasets as as defined in the datatypes_conf.xml configuration file. I could add the igvtools index command if the galaxy implicit indexing is not sufficient. Thanks, JJ On 1/24/13 9:49 AM, Jorge Sepulveda MD, PhD wrote: > Hi, Jim, > > I very much appreciate your galaxy wrappers for igvtools. I was wondering why you did not include the igvtools indexer. I tried to make a wrapper for it but it did not work. Your help will be much appreciated! > > > Jorge Sepulveda, MD, PhD > Associate Director for Laboratory Medicine, > Medical Director of Laboratory Informatics, > Columbia University Medical Center > Associate Professor, > Department of Pathology & Cell Biology > Columbia University College of Physicians and Surgeons > PH1590B > 622 W 168 St <x-apple-data-detectors://0> > New York, NY 10032 <x-apple-data-detectors://0> > Cell: (917) 862-6050 <tel:347-891-1122> > Office: 212-305-6360 <tel:212-305-6360> > E-mail:jls2282@columbia.edu <mailto:jls2282@columbia.edu> > > >

1 0

Medicago truncatula genome
by Senhao Zhang 24 Jan '13

24 Jan '13

Dear Galaxy Team, My name is Senhao Zhang, I am a graduate student from China. We're working on alfalfa's NGS project. Unfortunately, the genome of alfalfa is not available at present. The related model species Medicago truncatula's genome had been sequenced. Would you mind adding the Medicago truncatula genome into Galaxy? That would be highly appreciated. Thank you very much. Yours sincerely, Senhao

1 0

Questions about tool wrapping
by Jean-Frédéric Berthelot 24 Jan '13

24 Jan '13

Hi list, I am currently writing a Galaxy wrapper (for SortMeRNA [1]) and I would have several questions. == Pre-processing an input == SortMeRNA filters rRNA reads against an indexed rRNA database. This database can either be one bundled together with SortMeRNA and defined in a relevant .loc file, or one from the history. Either way, it must have been processed beforehand with another binary (just like makeblastdb/blastp). I am not sure of the best design here. * Providing another wrapper for this other binary, with users explicitly using it beforehand in their workflow? *Assuming the databases have been processed outside of Galaxy beforehand ? (As the tool relies on the file name, this would work for databases in the .loc file but not ones from the history) *Providing an extra-smart wrapper which would check if the database has been indexed, and if not invisibly indexing before running SortMeRNA ? == Error handling == I have been trying to use <stdio><regex> to catch an error (the one defined in above section actually) and inform the user with a meaningful message. >From the console debug, it seems the error is correctly detected, since it displays the custom <regex description=""> : galaxy.jobs INFO 2013-01-22 19:02:04,198 Job 202: Fatal error: The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA. But Galaxy only displays in the failed history a generic message « tool error An error occurred running this job: Unable to finish job » Am I missing something, or the <stdio><regex> is not meant to be used this way? == Using a previously set choice to set a default value later == Main option Alpha (a binary choice A/B) influence the default value of advanced option Beta (a float). Beta is buried into the "advanced options" section − I’d rather not have it just next to Alpha. Mirroring constructs seen in the <action>tag, I was hoping to do something like : <conditional name="Alpha"> <param name="Alpha_selector" type="select" format="text"> <option value="A">Option A</option> <option value="B">Option B</option> </param> </conditional> […] <conditional name="Alpha.Alpha_selector"> <when value="A"> <param name="Beta" type="float" value="0.15"/> </when> <when value="B"> <param name="Beta" type="float" value="0.25"/> </when> </conditional> But that does not seem to work. Am I missing something, or is it just not possible ? Alternatively, I looked into setting some hidden variable $default_value in the Alpha select, which would be used as <param name="Beta" value=$default_value/>, but that does not seem to work either Thanks for your help! [1] <http://bioinfo.lifl.fr/RNA/sortmerna/> -- Jean-Frédéric Bonsai Bioinformatics group

3 7

Jobs status not being updated
by Joachim Jacob |VIB| 24 Jan '13

24 Jan '13

Hi all, After updating to the latest Galaxy dist-release (and moving our server to a new location - but this can not be the reason I think), the status of the jobs are not being updated. The box in the history stays grey. After restarting Galaxy or the server, the correct status of the job is displayed. Any advice on how to proceed is appreciated. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

1 1