- galaxy-dev - lists.galaxyproject.org

print out workflow execution commands!
by Hakeem Almabrazi 30 Apr '13

30 Apr '13

Hi everyone, Is there an easy way to view/save/print out the executed commands and their parameters for a workflow? I want to see what is going on for certain steps in my workflow. Regards, Hak

2 5

Galaxy API prob with HTTP_REMOTE_USER
by Fabien Mareuil 30 Apr '13

30 Apr '13

Hi all, We encountoured an error with the galaxy api since the last galaxy-dist revision. here is an example of a command line that doesn't work (xxx stand for the admin key) : ./display.py xxxxxxxxxxxxxxxxxxxxxxxxxx http://localhost:18084/api/users we obtain the following error: HTTP Error 500: Internal Server Error As you can see, the request is done locally, without going through a proxy or apache. The galaxy log is the following: 127.0.0.1 - - [23/Apr/2013:19:55:26 +0200] "GET /api/users?key= xxxxxxxxxxxxxxxxxxxxx HTTP/1.1" 500 - "-" "Python-urllib/2.6" Error - <type 'exceptions.AssertionError'>: use_remote_user is set but no HTTP_REMOTE_USER variable Do you have an idea to solve this problem? Thank in advance for your answer. Best regards -- Fabien Mareuil | Centre d'Informatique pour la Biologie fabien.mareuil(a)pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux 75015 Paris, France

4 15

Tophat for Illumina is not running
by lilach noy 30 Apr '13

30 Apr '13

Hello, I'm new to Galaxy so I think i'm at the right place asking this, though please let me know if I got it all wrong. I sent a Tophat query on Thursday about 5 days ago and it is still waiting to ran (gray background). Is to O.k? A bug? Should i keep waiting or stop everything and restart? If this is not the address for reporting a suspicious bug, whom does this concern? Thank you very much, Lilach

2 1

Bug or design? Unit tests use *.loc rather than *.loc.sample
by Peter Cock 30 Apr '13

30 Apr '13

Hello all, Given the precedent that the test framework uses tool_conf.xml.sample rather than tool_conf.xml, I would expect it to use example.loc.sample rather than example.loc when running unit tests with parameters whose values come from a loc file. This is not the case. When writing unit tests of the Tool Shed, we can assume that as part of the automated installation example.loc will be generated from the supplied example.loc.sample file - and so for things like the nightly automated testing on the Tool Shed, the files will be the same. However, on real Galaxy installations, the administrator will likely edit example.loc and it will not match example.loc.sample any more. This means that for writing a unit test, I cannot make any assumptions about the contents of example.loc, but it would be reasonable to expect example.loc.sample setup will still match the unit tests. Is it sensible to make the test framework load *.loc.sample rather than *.loc for this reason? If not, how exactly are unit tests dependent on values in a loc file meant to be written? This is a problem for me writing tests for Blast2GO (property files in blast2go.loc), BLAST+ (databases in blastdb.loc etc). It hasn't yet been a problem for Effective T3 as here my effectiveT3.loc file still matches the sample file. Thanks, Peter

1 0

Teaching using Galaxy
by David Joly 30 Apr '13

30 Apr '13

Hi everybody! I am currently creating a "bioinformatics" course for undergraduate (biology students with no knowledge of programming). I would like to use Galaxy as their everyday platform where they would learn the basics and use the appropriate tools (BLAST and databases, multiple alignment, phylogenetics, dealing with "omics" data, and so on). Is there any available resources about using Galaxy for teaching (undergraduates)? Any suggestions of good textbooks? Not a Galaxy textbook of course, but a "bioinformatics textbook" that would be a good companion to help the students understand the basics behind the tools. Thanks, DJ

4 6

Using conditional parameters in unit tests
by Peter Cock 30 Apr '13

30 Apr '13

Hi all, I've not previously need to use a conditional parameter in a unit test, but for the MIRA wrapper this is essential. Here's my first attempt and the error when running the test: https://bitbucket.org/peterjc/galaxy-central/commits/794ebc6cafecd3db9388f5… <tests> <test> <param name="job_method" value="denovo" /> <param name="job_type" value="est" /> <param name="job_qual" value="accurate" /> <param name="condBackbone.use" value="false" /> <param name="condSanger.use" value="true" /> <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" /> <param name="condRoche.use" value="false" /> <param name="condIllumina.use" value="false" /> <param name="condIonTorrent.use" value="false" /> <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> </test> </tests> Note that I can't refer to the parameters by the final part of their name ("use") as this is ambiguous. The dot syntax is natural to match that used in the Cheetah templates, but does not appear to work in the tool tests: $ ./run_functional_tests.sh -id mira_assembler ... ====================================================================== ERROR: Assemble with MIRA v3.4 ( mira_assembler ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 76, in do_it page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs) File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 118, in __expand_grouping if declared_inputs[ value.test_param.name ] == case.value: KeyError: 'use' Is there something wrong with my test, or is this not yet supported? Thanks, Peter

3 7

Setting torque queues
by Scott Hazelhurst 30 Apr '13

30 Apr '13

Dear dev I would be grateful for some assistance in setting up our galaxy server to submit jobs to our torque server.. We are using release_2013.04.01 I have tried going through the install information but clearly I’ve misunderstood something, and unfortunately most examples come from earlier versions galaxy.jobs DEBUG 2013-04-30 15:28:13,481 (33) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/33 galaxy.jobs.handler DEBUG 2013-04-30 15:28:13,527 (33) Dispatching to pbs runner 146.141.75.218, 146.141.1.81 - - [30/Apr/2013:15:28:12 +0200] "POST /galaxy/tool_runner/index HTTP/1.1" 200 - "http://galaxy.bioinf.wits.ac.za/galaxy/tool_runner/rerun?id=9752b387803d3e1e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:20.0) Gecko/20100101 Firefox/20.0" galaxy.jobs DEBUG 2013-04-30 15:28:14,213 (33) Persisting job destination (destination id: WitsLong) Exception AssertionError: AssertionError('State <sqlalchemy.orm.state.InstanceState object at 0x7f79682e5150> is not present in this identity map',) in <bound method InstanceState._cleanup of <sqlalchemy.orm.state.InstanceState object at 0x7f79682e5150>> ignored galaxy.jobs.handler INFO 2013-04-30 15:28:14,522 (33) Job dispatched galaxy.tools DEBUG 2013-04-30 15:28:15,189 Building dependency shell command for dependency 'clustalw2' galaxy.tools WARNING 2013-04-30 15:28:15,192 Failed to resolve dependency on 'clustalw2', ignoring galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:15,957 (33) submitting file /home/galaxy/galaxy-dist/database/pbs/33.sh galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:15,958 (33) command is: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/home/galaxy/galaxy-dist/database/files/000/dataset_2.dat" -o "/home/galaxy/galaxy-dist/database/files/000/dataset_60.dat" -s "ALIGNED" -l "/home/galaxy/galaxy-dist/database/files/000/dataset_61.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL" galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:15,963 (33) pbs_submit failed (try 1/5), PBS error 15039: Route rejected by all destinations galaxy.jobs DEBUG 2013-04-30 15:28:16,400 (34) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/34 galaxy.jobs.handler DEBUG 2013-04-30 15:28:16,416 (34) Dispatching to pbs runner 146.141.75.218, 146.141.1.81 - - [30/Apr/2013:15:28:13 +0200] "POST /galaxy/tool_runner/index HTTP/1.1" 200 - "http://galaxy.bioinf.wits.ac.za/galaxy/tool_runner/rerun?id=9752b387803d3e1e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:20.0) Gecko/20100101 Firefox/20.0" galaxy.jobs DEBUG 2013-04-30 15:28:16,668 (34) Persisting job destination (destination id: WitsLong) galaxy.jobs.handler INFO 2013-04-30 15:28:16,689 (34) Job dispatched galaxy.tools DEBUG 2013-04-30 15:28:16,937 Building dependency shell command for dependency 'clustalw2' galaxy.tools WARNING 2013-04-30 15:28:16,938 Failed to resolve dependency on 'clustalw2', ignoring galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:17,160 (34) submitting file /home/galaxy/galaxy-dist/database/pbs/34.sh galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:17,161 (34) command is: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/home/galaxy/galaxy-dist/database/files/000/dataset_2.dat" -o "/home/galaxy/galaxy-dist/database/files/000/dataset_62.dat" -s "ALIGNED" -l "/home/galaxy/galaxy-dist/database/files/000/dataset_63.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL" galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:17,162 (34) pbs_submit failed (try 1/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:17,971 (33) pbs_submit failed (try 2/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:19,166 (34) pbs_submit failed (try 2/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:19,975 (33) pbs_submit failed (try 3/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:21,170 (34) pbs_submit failed (try 3/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:21,978 (33) pbs_submit failed (try 4/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:23,173 (34) pbs_submit failed (try 4/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:23,982 (33) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:25,176 (34) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs ERROR 2013-04-30 15:28:25,984 (33) All attempts to submit job failed galaxy.jobs.runners.pbs ERROR 2013-04-30 15:28:27,179 (34) All attempts to submit job failed <table width="100%" border="0" cellspacing="0" cellpadding="0" style="width:100%;"> <tr> <td align="left" style="text-align:justify;"><font face="arial,sans-serif" size="1" color="#999999"><span style="font-size:11px;">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. </span></font></td> </tr> </table

1 0

Visually differentiate the main and test Tool Shed
by Peter Cock 30 Apr '13

30 Apr '13

Hello all, I can't be the only Galaxy Tool author to have accidentally made a change on the main Tool Shed my mistake, wrongly assuming I was on the test Tool Shed (sandbox). In this case the tool update was harmless, but it could easily have resulted in users of my tool downloading a broken file. To minimise the chances of this happening again, please: (1) Change the page title of the http://testtoolshed.g2.bx.psu.edu/ which is currently also "Galaxy Tool Shed". I'm talking about the title attribute shown in the Web Browser tab or chrome. (2) Change the colour scheme of http://testtoolshed.g2.bx.psu.edu/ which is identical to the main tool shed. How about red? Related to this, you could replace Galaxy icon with a "beta" or something? http://testtoolshed.g2.bx.psu.edu/static/images/galaxyIcon_noText.png Thanks, Peter

2 2

BLAST Database error: No alias or index file found
by Mike Dyall-Smith 30 Apr '13

30 Apr '13

This follows on from Kenneth Auerbach's question Sep 12, 2012: Galaxy error running NCBI BLAST: blastx http://dev.list.galaxyproject.org/Galaxy-error-running-NCBI-BLAST-blastx-td… I wish to use a local copy of the genbank database for searches. The genbank db files are sitting in a folder on an external drive, and I have altered the blastdb_p.loc to point to them. I can see and select this database within galaxy, but when I try using blast+ blastp tool, I get the error ""BLAST Database error: No alias or index file found for protein database [/media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr] in search path [/var/lib/galaxy-server/database/job_working_directory] As suggested previously by Peter Cock, I can list all the files with: ls /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr* which gives me the list: /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phr /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pin /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pnd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pni /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pog /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.ppd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.ppi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.psd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.psi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.psq ... /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.phd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.phi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.phr /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pin /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pnd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pni /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pog /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.ppd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.ppi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psq /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.pal The alias file, nr.pal is the last one in the list above, so is present. I changed the default directory for the blast database: BLASTDB=/media/sf_mikeds_bioinf/GenbankDB_Files/nr - this made no difference to the error. I am running biolinux 7 (latest) in ubuntu within VirtualBox, on a macbook pro. The external drive is a shared folder, and I can see all the files within galaxy (e.g. I can import data data files). Any help would be appreciated. Regards, Mike DS

2 1

Re: [galaxy-dev] gff installation failed with easy_install
by Brad Chapman 30 Apr '13

30 Apr '13

Mic; > I have tried to install gff with easy_install, but I got the following > error: > $ easy_install --prefix=/home/mic/apps/pymodules -UZ > https://github.com/chapmanb/bcbb/tree/master/gff > Downloading https://github.com/chapmanb/bcbb/tree/master/gff > error: Unexpected HTML page found at > https://github.com/chapmanb/bcbb/tree/master/gff > > How is it possible to install gff? I don't know of a way to install directly from git with subdirectories like that. You'd need to clone, then install with easy_install or pip: $ git clone git://github.com/chapmanb/bcbb.git $ easy_install bcbb/gff $ pip install bcbb/gff Apologies about the convoluted setup. Depending on what you're doing, you might want to have a look at gffutils: https://github.com/daler/gffutils We're working on rolling the functionality from the gff library into this so there'll be one place to work from for GFF in python. Hope this helps, Brad

2 1