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

Tool params passed to python dynamic job runner
by Ganote, Carrie L 14 Aug '13

14 Aug '13

Hi List, I've run into a frustration recently with passing values to the dynamic job runner from a tool. Here's what's going on: in ncbi_blastn_wrapper.xml: <param name="pathToModule" type="hidden" value="/abs/path/to/module" /> ... in dynamic_runner.py: ... def blastn_wrapper(job): incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] ) modulePath = incoming["pathToModule"] modulePath.replace("\"", "").strip() dummy = '/abs/path/to/module' equals = (modulePath == dummy) log.debug( '\n~%s~\n~%s~\nsame? %s' % (mypath, dummy, equals) ) ... log: ~"/abs/path/to/module"~ ~/abs/path/to/module~ same? False I have no idea why these "" are persisting, or if that is even the problem. I can't find the modulePath when using os.path.exists(modulePath). What I want to do is optionally (user checks a box) run another python script that splits up the blast queries into a bunch of jobs and submits each job separately - and I was just going to import this other script using sys.append(modulePath) in some poor attempt to keep the system cleaner. If this is a problem with my understanding of python, please enlighten me - if there are other tools that pass around paths or if there's another way to do this in less hacky way, I'm open to advice. Thanks! Carrie Ganote

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adding reference genome
by Vijay Kumar 13 Aug '13

13 Aug '13

Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u

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ENA galaxy import link broken?
by Andrew Warren 13 Aug '13

13 Aug '13

Hello, I am trying to use the ENA galaxy import feature. This involves going to the analyze menu in galaxy and clicking the link 'EBI SRA' which is encoded as http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=https%3A//main.g2.bx.psu.ed… This does not seem to be working at present. I manage a Galaxy site that uses a similar setup encoded as (also doesn't work) http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=http%3A//rnaseq.pathogenpor… I sent an email off to ENA but haven't got a response. Any ideas? Thanks for any help, Andrew Warren

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Cloudman could not determine the version of Tophat and cufflinks.
by Anto Praveen Rajkumar Rajamani 13 Aug '13

13 Aug '13

Hello, Along with the Tophat (could not determine version: http://dev.list.galaxyproject.org/Problems-with-Tophat-amp-uploading-files-…) problem in my cloudman, I experience a similar problem with Cufflinks. I uploaded a trial BAM file and ran cufflinks 0.0.6. The run failed and I got a message that "Could not determine the version of Cufflinks". When I tried to report the bug using the green bug icon, I get a message "Mail is not configured to report this bug". I updated my Galaxy to http://bit.ly/galaxy20130812 and restarted my instance. My instance is on, but I am unable to analyse my data. Where do I go wrong? Kindly help me to solve this problem. Thank you. Best wishes, Anto

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Urgent Help Required.....Fastq file
by Vengurlekar, Priyanka (NIH/NCI) [C] 13 Aug '13

13 Aug '13

Hello, I am trying to upload this following file on galaxy and den use the barcode splitter....but it does not upload the file at all. I followed you videos to upload the data too and i am using browse to upload this fastq file. would like you to try to upload and let me know if it works if not why doesnt it work. I tried two other files too. and they too cannot be uploaded it turns red in color immediately. can you tell me why as this is very important.Thanking you, Sincerely, Priyanka.V

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Join the HOMER Galaxy wrapper development!
by Bjoern Gruening 13 Aug '13

13 Aug '13

Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc files to define different HOMER datasets - macros - compostite datatypes (html output) I think that project can be a good start to learn Galaxy Tool development with all its simple and enhanced features. Also HOMER is a complex suite and you can add small and really big features if you like. If you are interested but did not have any experience in Tool development, do not hesitate to ask. I will try to help and explain as much as I can. For the beginning I included only 3 tools, and only one of them with a bunch of parameters. So there are many things to do ... If anyone is interested in leaning Galaxy Tool development and want to contribute. Fell free to join and contact me. Cheers, Bjoern P.S. I do not mind to merge my changes to the already existing repository from Kevin, but I was not able to contact him. http://toolshed.g2.bx.psu.edu/view/kevyin/homer

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Running Jobs:
by Jurgens de Bruin 13 Aug '13

13 Aug '13

Hey All, Apologies for all the questions on the mailing list...I am having a lot of difficulty getting our local Galaxy working. Currently I have galaxy running but when I try run a job it just stays on "Job is waiting to run" and never runs. I have read the guide and wiki but can't seem to solve my problem at all... The output of sh run.sh: sh run.sh /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/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: /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/boto-2.5.2-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Whoosh-0.3.18-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/amqplib-0.6.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pexpect-2.4-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Babel-0.9.4-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Mako-0.4.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebHelpers-0.2-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebOb-0.8.5-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Routes-1.12.3-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/wchartype-0.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/elementtree-1.2.6_20050316-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/docutils-0.7-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/PasteDeploy-1.5.0-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Paste-1.7.5.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/lib, /scratch/sysusers/galaxy/galaxy_env/lib64/python26.zip, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/plat-linux2, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-tk, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-old, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-dynload, /usr/lib64/python2.6, /usr/lib/python2.6, /scratch/sysusers/galaxy/galaxy_env/lib/python2.6/site-packages /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname> Starting server in PID 59419. serving on 0.0.0.0:8989 view at http://127.0.0.1:8989 /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 155.240.187.100 - - [13/Aug/2013:12:28:36 +0000] "GET /root HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /root/welcome HTTP/1.1" 302 - "http://155.240.187.2:8989/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /history HTTP/1.1" 200 - "http://155.240.187.2:8989/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /history/get_display_application_links HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:30 +0000] "POST /tool_runner HTTP/1.1" 200 - "http://genome.ucsc.edu/cgi-bin/hgTables" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:30 +0000] "GET /history HTTP/1.1" 200 - "http://155.240.187.2:8989/tool_runner" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:31 +0000] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:31 +0000] "GET /history/get_display_application_links HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:35 +0000] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" I would I check to see if a job is passed on to torque via drmaa? Any help would be appreciated -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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Galaxy behind a authenticated proxy Server
by Jurgens de Bruin 13 Aug '13

13 Aug '13

To All, I am in the process of setting-up a local galaxy server. To access the internet we are required to go trough a authenticated proxy server before any web-services can be accessed. So my questions is how will galaxy handle this? -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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scripting galaxy installs / toolshed
by Ido Tamir 13 Aug '13

13 Aug '13

Hi, we would like to coordinate with another institution and their galaxy setup regarding tools installed from multiple toolsheds (and their position/group in the panel) should be similar. Is there a way to achieve that with scripting? Suppose I would start the galaxy install from scratch also at our site. Could we somehow coordinate our installation? thank you very much, ido

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Error when running test
by Jurgens de Bruin 13 Aug '13

13 Aug '13

Hi All, I am getting the following error in run_functional_tests.html when running sh run_functional_tests.sh. Any idea what is happening? Thanks Traceback (most recent call last): File "/usr/lib64/python2.6/unittest.py", line 269, in run self.setUp() File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/test/base/twilltestcase.py", line 53, in setUp self.home() File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/test/base/twilltestcase.py", line 1141, in home self.visit_url( self.url ) File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/test/base/twilltestcase.py", line 1324, in visit_url tc.code( 200 ) File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 133, in code should_be)) TwillAssertionError: code is 401 != 200 -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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