galaxy-dev January 2013

galaxy-dev@lists.galaxyproject.org

105 participants
195 discussions

Re: [galaxy-dev] anybody seen 403s after a recent upgrade?
by Langhorst, Brad 10 Jan '13

10 Jan '13

grr - actually - no it's not fixed I didn't see it on a few refreshes, but apparently it was temporary - or I was hallucinating. brad On Jan 9, 2013, at 3:27 PM, Brad Langhorst <Langhorst(a)neb.com> wrote: > Hmmm > I reconsulted the docs and commented these lines. All seems well again after an apache restart. > I had been running like this for a year or more, and only observed problems after the most recent update > > > # RewriteCond %{IS_SUBREQ} ^false$ > # RewriteCond %{LA-U:REMOTE_USER} (.+) > # RewriteRule . - [E=RU:%1] > RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e > > I just cargo culted those in to begin with… I don't really know what they do. > > > Brad > > On Jan 9, 2013, at 1:21 PM, Nate Coraor <nate(a)bx.psu.edu> > wrote: > >> On Jan 7, 2013, at 10:43 PM, Langhorst, Brad wrote: >> >>> galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langhorst(a)neb.com' invalidating session >>> 10.254.254.86 - - [07/Jan/2013:22:06:30 -0400] "GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1" 403 - "http://galaxy.neb.com/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20100101 Firefox/17.0" >> >> Hi Brad, >> >> Your proxy server appears to no longer be passing the REMOTE_USER header correctly. Did anything change there? >> >> --nate >> >>> >>> i did not observe this before today… but maybe I've screwed things up in my hg fiddling today. >>> Did anybody else see this? >>> >>> manual refreshes work, but automatic ones don't >>> >>> >>> Brad >>> -- >>> Brad Langhorst >>> langhorst(a)neb.com >>> >>> >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> > > -- > Brad Langhorst > langhorst(a)neb.com > > > > > -- Brad Langhorst langhorst(a)neb.com

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GATK tools / Realigner Target Creator / pb to create java virtual machine
by Sarah Maman 10 Jan '13

10 Jan '13

Hello, When we run "Realigner Target Creator <http://sigenae-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gatk_r…> for use in local realignment" , I have this error : *Dataset 19: Realigner Target Creator on data 5, data 6, and data 4 (GATK intervals)* Tool execution generated the following error message: Could not create the Java virtual machine. The tool produced the following additional output: Epilog : job finished at jeu. janv. 10 14:49:10 CET 2013 So I have addded java -Xmx4G " in realigner_target_creator.xml file but the problem is not solved. Do you have any idea ?? Thanks in advance, Sarah

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Re: [galaxy-dev] Installing dependencies from toolshed fails and produces strange folder
by Joachim Jacob 10 Jan '13

10 Jan '13

Thanks Dave, for letting me see the more useful stuff you can do with env.sh. Unfortunately, env.sh is not available in that tool_dependency_dir after installing the dependencies. I had my path set between quotes in the universe_wsgi.ini, producing unwanted results (the ' folder). (fe, tool_dependency_dir = '/apps'). Hence, the dependencies were installed in a place I did not want to - I moved them to the right path. BUT, no env.sh is in that folder. I cannot reinstall the dependencies via the interface neither. The quick fix I want to avoid, setting all paths hardcoded in picard tools :-/ [galaxy@galaxy e0232cbac965]$ pwd /apps/picard/1.56.0/devteam/picard/e0232cbac965 [galaxy@galaxy e0232cbac965]$ ll -alh total 12K drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 . drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 .. drwxrwxr-x 2 galaxy galaxy 4.0K Jan 8 15:07 jars I created a simple env.sh myself in that folder, but no avail. #!/bin/bash JAVA_JAR_PATH=`pwd`/jars Small question: should there not be included in the tool's xml file a statement: <requirement type="set_environment">JAVA_JAR_PATH</requirement> See http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28env.sh%29 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 On 01/08/2013 05:53 PM, Dave Bouvier wrote: > Joachim, > > JAVA_JAR_PATH is set in env.sh, which is generated during the tool > dependency installation process and saved to > <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/env.sh > > The install code sets this variable to > <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/jars > > --Dave B. > >> *From: *Joachim Jacob <joachim.jacob(a)vib.be >> <mailto:joachim.jacob@vib.be>> >> *Date: *January 8, 2013 11:06:17 AM EST >> *To: *Greg Von Kuster <greg(a)bx.psu.edu <mailto:greg@bx.psu.edu>> >> *Subject: **Re: [galaxy-dev] Installing dependencies from toolshed >> fails and produces strange folder* >> *Reply-To: *joachim.jacob(a)vib.be <mailto:joachim.jacob@vib.be> >> >> Thanks. And where is the JAVA_JAR_PATH set? >> >> Joachim >> >> Joachim Jacob >> >> Rijvisschestraat 120, 9052 Zwijnaarde >> Tel: +32 9 244.66.34 >> Bioinformatics Training and Services (BITS) >> http://www.bits.vib.be >> @bitsatvib >> >> On 01/08/2013 04:55 PM, Greg Von Kuster wrote: >>> Hello Joachim, >>> >>> Tool dependencies are installed into the location defined by the >>> following entry in your universe_wsgi.ini file. >>> >>> # Path to the directory in which managed tool dependencies are >>> placed. To use >>> # the dependency system, see the documentation at: >>> # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies >>> tool_dependency_dir = ../tool_dependencies >>> >>> Greg Von Kuster >>> >>> On Jan 8, 2013, at 10:45 AM, Joachim Jacob wrote: >>> >>>> Hi all, >>>> >>>> >>>> Updating our Galaxy: the migration of some tools to the toolshed >>>> (let's take picard as an example) and installing them back from the >>>> toolshed worked well. >>>> However, during the update, I forgot to install the dependencies. >>>> >>>> So I went to the administration part of our Galaxy, and selected >>>> 'Manage installed tool shed repositories >>>> <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. >>>> With the interface, I installed the dependencies for the tool (*Tool >>>> shed repository 'picard' tool dependencies*): but this failed with >>>> an error (SystemError: 1 or something alike). >>>> >>>> After this error, I noticed a strange folder was created in the >>>> Galaxy root called '. Meaning, really called ', like "'" :-) >>>> $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars >>>> >>>> The installer installed all jars in this folder. I am currently >>>> looking into the code, but my first reflex was to think: the path is >>>> not correctly set, so heading to universe_wsgi.ini! But this seemed >>>> to be a wrong guess. Any idea what parameters are wrongly set here? >>>> >>>> >>>> Cheers and 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 >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>> >> > >

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Maq-error
by gen0224 10 Jan '13

10 Jan '13

Hi, I am a beginner to Maq. Now, I am mapping reads to transcripts by Maq. But, there ara some errors. I need some help. -- CMD: /usr/local/bin/maq fasta2bfa /home/transcripts.fasta ./test/ref.bfa 2> /dev/null -- CMD: /usr/local/bin/maq fastq2bfq -n 2000000 /home//A_1000.fq ./test/read1 -- finish writing file './test/read1(a)1.bfq' -- 2500 sequences were loaded. -- CMD: (cd ./test; /usr/local/bin/maq map -n 2 -e 70 -u unmap1(a)1.txt aln1(a)1.map ref.bfa read1(a)1.bfq 2> aln1(a)1.map.log) sh: line 1: 29654 error /usr/local/bin/maq map -n 2 -e 70 -u unmap1(a)1.txt aln1(a)1.map ref.bfa read1(a)1.bfq 2> aln1(a)1.map.log ** fail to run command '(cd ./test; /usr/local/bin/maq map -n 2 -e 70 -u unmap1(a)1.txt aln1(a)1.map ref.bfa read1(a)1.bfq 2> aln1(a)1.map.log)' at /usr/local/bin/maq.pl line 842. Best, Jingen gen0224，jingen.li87(a)gmail.com 2013-1-10

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anybody seen 403s after a recent upgrade?
by Langhorst, Brad 09 Jan '13

09 Jan '13

galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langhorst(a)neb.com<mailto:langhorst@neb.com>' invalidating session 10.254.254.86 - - [07/Jan/2013:22:06:30 -0400] "GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1" 403 - "http://galaxy.neb.com/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20100101 Firefox/17.0" i did not observe this before today… but maybe I've screwed things up in my hg fiddling today. Did anybody else see this? manual refreshes work, but automatic ones don't Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Blank local reference - even after following NGS installation instructions
by Jorge Sepulveda 09 Jan '13

09 Jan '13

Hi, I set up a local galaxy in my MacPro on 1/3/2013 using: hg clone https://bitbucket.org/galaxy/galaxy-dist/ into this directory: ~/ngs/applications/galaxy-dist Indexed hg19.fa using bwa index to ~/ngs/refgenomes/hg19/bwa_indexed/ -rw-r--r-- 1 JS staff 6597 Jan 2 15:03 hg19.fa.amb -rw-r--r-- 1 JS staff 6844 Jan 2 15:03 hg19.fa.ann -rw-r--r-- 1 JS staff 3101804844 Jan 2 15:02 hg19.fa.bwt -rw-r--r-- 1 JS staff 775451186 Jan 2 15:03 hg19.fa.pac -rw-r--r-- 1 JS staff 1550902424 Jan 2 15:06 hg19.fa.sa Added: hg19 hg19 hg19 ~/ngs/refgenomes/hg19/bwa_indexed/hg19 to this file: ~/ngs/applications/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/tool-data/bwa_index.loc BWA shows up on the galaxy tools list, but the local reference genome box remains empty. It runs fine when I use a reference sequence (chr22.fa) from history. If I download bwa (or bowtie2) and install according to the steps in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I have the same problem (empty local reference). What am I missing? 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 New York, NY 10032 Cell: (917) 862-6050 Office: 212-305-6360 E-mail:jls2282@columbia.edu

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Transfer Manager
by Kyle Ellrott 09 Jan '13

09 Jan '13

Is there any documentation on the transfer manager? Is this a mechanism that I could use to synchronize data libraries between two different Galaxy installations? Kyle

3 4

Tool tests
by Cameron Jack 09 Jan '13

09 Jan '13

Hi, I hope I'm writing to the right area (if not, please point me in the right direction and I'll go on my way). I have a set of tools that our team have built and been using for functional genomics analysis, which I would like to integrate into Galaxy. My first concern is with the tests. Our code is unit tested but one script is tasked with downloading gene sets from Ensembl. We have a local copy of much of the Ensembl DB (5TB worth) and even this is fairly slow to pull from (5-10 mins). Pulling from the publicly available Ensembl site would be horrifically slow. Since it's stated here: http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests that functional tests are required, I'm looking for suggestions as to how to meet this requirement without taking up an hour of the test runner's time (for one tool). My second question is if a file is produced by a script and given a specific name based on its inputs, how should I (if at all) define the output of this script. My last question is "how much functional testing is required?". I have a script here whose job is to produce plots of data. There are about 30 command-line options and many of these have multiple choices available to them. Do I need to provide functional tests for every one of these? I can imagine having to provide 100 PNG files to compare my output again.... I have searched for answers to the above (made much more tricky thanks to Samsung), I don't wish to waste anyone's time. Many thanks in advance, Cameron

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File import recovery
by Kyle Ellrott 09 Jan '13

09 Jan '13

I'm currently adding a large number of files into my Galaxy instance's dataset library. During the import some of the files (a small percentage) failed with: /inside/depot4/galaxy/set_metadata.sh: line 4: 14790 Segmentation fault (core dumped) python ./scripts/set_metadata.py $@ I think it's probably standard cluster shenanigans, and may work just fine if run again. But there doesn't seem to be a way retry. Is there a way to deal with this that is easier than manually deleting and re-uploading the offending files? Kyle

2 3

Galaxy submitting jobs to remote cluster
by Thomas Uram 09 Jan '13

09 Jan '13

Hello: I am trying to configure Galaxy to submit jobs to a remote cluster (specifically, an XSEDE resource to which I don't have administrative access). I'm familiar with LWR and have read another response about configuring the Galaxy host as a PBS submit host. What is the best approach to accomplish what I'm after? I have experimented with the cli job runner with the SecureShell and Torque plugins. With some minimal modifications, I can run jobs via this mechanism, but file staging fails. I haven't looked into the details of the staging failure yet. Is this a viable approach? Is the cli job runner supported? (the universe_wsgi.ini file says available job runners include pbs and drmaa) I've found a similar question on the galaxy-dev mailing list, with mention of some relevant recent work: http://dev.list.galaxyproject.org/Remote-Job-Submission-from-Local-Install-… What is the status of the work referenced in that post? Thanks, Tom Uram

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galaxy-dev January 2013