[galaxy-dev] Submitting jobs with PBS
Hi !! I've got a problem with PBS when I want to submit a job to our cluster with Galaxy. Every time, PBS says me pbs_submit failed, PBS error 15023: Bad user - no password entry. Indeed, Galaxy uses my email address (used in Galaxy) as user by default ! But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner user and not my email… Is it possible to set the owner user as previous Galaxy version ? (I found the drmaa_external_* session in universe but I don't really understand how to configure this part…). Thanks a lot, Best Regards BRAS Marc ___ 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/
Re: [galaxy-dev] HMMER wrappers
On Fri, May 25, 2012 at 4:54 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Edward, It has taken me a while but I'm how trying to use HMMER3, and do so from within Galaxy. I've realised that the per sequence and per domain tables from hmmscan and hmmsearch (via the --tblout and --domtblout switches) are NOT tab separated, but space separated to give an eye pleasing column based layout. However, your wrapper tells Galaxy they are tabular. As a result, Galaxy treats them like tables with one column, which means all the table operations like filtering on a particular column are not possible. Has this not affected your users? I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT3 (semi-colons). Would you agree that a wrapper script to reformat the HMMER3 tables into tab-separated tables would be the best solution? Would you accept a code contribution to do this? Regards, Peter Hi Edward, I've written a simple HMMER3 table to tabular script in Python, https://github.com/peterjc/picobio/blob/master/hmmer/hmmer_table2tabular.py Would you prefer to: (a) amend the XML to call HMMER, and then call the conversion script twice. (b) turn this into a single wrapper script which calls HMMER3 and then converts the two tables (using a multiple command line call with shell semi-colon separators). (c) do something else? I favour the wrapper script option as more flexible in the long run (e.g. for error handling and splitting jobs over multiple machines), and the multiple command approach may lead to overly long command line strings. Peter ___ 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/
[galaxy-dev] Galaxy
Hello all, I would like to learn Galaxy and more, as my interest is in Bioinformatics and computational research.Please any help for tutorial materials Thank you in advance Twaha ___ 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/
Re: [galaxy-dev] BWA Problem
Hi, Have you created the index files using the exact same version of bwa? I've had segfaults when using references indexed on a different computer running a different version. Geert On 05/28/2012 08:54 PM, CHEBBI Mohamed Amine wrote: Hi ! I have a problem when i execute BWA from my local galaxy instance. I have this error message : An error occurred running this job:/BWA Version: 0.6.1-r104 Error indexing reference sequence. [bwa_index] Pack FASTA... 2.35 sec [bwa_index] Construct BWT for the packed sequence... Segmentation fault/ / / Could anyone help me to fix it thanks ! Regards Amine ___ 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/ ___ 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/
[galaxy-dev] Uncaught exception when submitting jobs
Hi,All of a sudden I am getting these errors when I submit a job in my Galaxy system.I can't recall I changed anything and I checked the universe file but nothing obvious there...Any ideas?ThanksThongalaxy.jobs.runners.drmaa ERROR 2012-05-29 09:40:46,873 Uncaught exception queueing jobTraceback (most recent call last): File "/home/tdeboer/code/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 133, in run_next self.queue_job( obj ) File "/home/tdeboer/code/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 213, in queue_job job_id = self.ds.runJob(jt) File "/home/tdeboer/code/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/home/tdeboer/code/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File "/home/tdeboer/code/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))DeniedByDrmException: code 17: ERROR! invalid option argument ""___
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Re: [galaxy-dev] Batch limit on Wokflows
Unfortunately this is one of the most glaring problems with the UI based workflow engine that is Galaxy (That, and no modular workflows)...You cannot easily pair up more than one set of paired end reads from the UI, you need to use the API to run pairs of FASTQ files like that...I have written a script that will do this through the API..Excerpt below...You won't be able to run this as-is, but it gives you some idea what hoops you have to jump through to do this..The section INPUT FILE DEFINITION is the meat of the script, in that I simply cycle through all the files in a Library and match up the files myself...Ugly but it worksThoncode#!/usr/bin/env python# MUT190-1.py## Version 2.0.0# Created: 5-Apr-2012# By Thon de Boer, GHI# Last Update: 23-Apr-2012# By Thon de Boer, GHI## This program will run step MUT190-1; the alignment of FASTQ file with BWA# It is based on the generic GALAXY Workflow execution engine,# but has hardcoded defaults, seen below## Version 1.0.1: Added get_folder_id# Version 2.0.0: Made the config file an option (and the only option)#"""Execute a specifc workflow on a specific set of history items.It is created for running the GATK pipeline on a selected set of paired-end readsInput to the tool is the name of a History and it will extract all the paired-end FASTQ files from this."""import os, sys, optparse, shutil, subprocess, tempfile, fileinput, psycopg2, ConfigParsersys.path.insert( 0, os.path.dirname( __file__ ) )sys.path.insert( 0, "/home/tdeboer/g/scripts/api" )from common import *from ThonsModules import *def main(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-c', '--config', dest='config', type='string', help='the configuration file containing all the settings for this workflow' ) parser.add_option( '-t', '--test', action='', dest='test', help='Do not submit, but test the settings', default=False) (options, args) = parser.parse_args() if not options.config:print "Error: No config file proivided. Please provide a configuration file with the -c,--config flag."sys.exit(1) config = ConfigParser.RawConfigParser() try:config.read(options.config)GALAXY_LIBRARY_FASTQ = config.get('GALAXY', 'GALAXY_LIBRARY_FASTQ').strip('"')GALAXY_WORKFLOW_DEFAULT=config.get('GALAXY', 'GALAXY_WORKFLOW_DEFAULT').strip('"')GALAXY_OUTHISTORY_DEFAULT=config.get('GALAXY', 'GALAXY_OUTHISTORY_DEFAULT').strip('"')galaxyURL=config.get('GALAXY', 'GALAXY_URL').strip('"')myKey=config.get('GALAXY', 'MYKEY').strip('"') except Exception, e:print 'Error: %s' % esys.exit(1) data = ""> #Find the files that go with the history or library try:historyPrefix = GALAXY_OUTHISTORY_DEFAULT + '-'files = {}lib_id = get_library(myKey, galaxyURL, GALAXY_LIBRARY_FASTQ)files = get_files_from_library(myKey, galaxyURL, GALAXY_LIBRARY_FASTQ, lib_id)if files == {}: print 'Error: Did not get any files from the library' sys.exit(1)workflow_id = get_workflow(myKey, galaxyURL, GALAXY_WORKFLOW_DEFAULT)data['workflow_id'] = workflow_id except Exception, e:print 'Error: %s' % esys.exit(1) data['ds_map'] ={} #Define the standard library datasets try:##### WORKFLOW STEP DEFINITION#####Format for these lines should be followed...Only change the 'BAITS' and 'MUT190/Baits and Targets/SS_Mut_v2_baits190.bed' textdata['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'BAITS')] = get_library_file(myKey, galaxyURL, 'MUT190/Baits and Targets/SS_Mut_v2_baitsMUT190.bed')data['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'TARGETS')] = get_library_file(myKey, galaxyURL, 'MUT190/Baits and Targets/SS_Mut_v2_targetsMUT190_PLUS60.interval')data['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'TARGETS (GATK)')] = get_library_file(myKey, galaxyURL, 'MUT190/Baits and Targets/SS_Mut_v2_targetsMUT190_PLUS400.gatk-interval')data['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'dbSNP VCF File')] = get_library_file(myKey, galaxyURL, 'Annotations/Annotations used in GATK-1.5/dbsnp_135.b37.vcf')data['ds_map'][get_workflow_step(myKey, galaxyURL, workflow_id, 'Mills_and_1000G_gold_standard')] = get_library_file(myKey, galaxyURL, 'Annotations/Annotations used in GATK-1.5/Mills_and_1000G_gold_standard.indels.b37.sites.vcf') except Exception, e:print "Error: Problem with finding all the input steps for this workflow: %s" % esys.exit(1) ### # # INPUT FILE DEFINITION # These are the files that are cycled over # ### for f in files:if '_R1.fastq' in f: f2 =
Re: [galaxy-dev] Unable to Load Any History From File
Todd, Errors when importing history archives are not exposed well right now. If you look at the job table in your Galaxy database, you should be able to see why the job failed. Using SQL like this should work: -- select * from job where tool_id='__export_history__' order by id desc limit 5; -- Alternatively, can you share a history archive that's failing and we can take a look? Thanks, J. On May 29, 2012, at 2:42 PM, Todd Oakley wrote: Hello, I want to be able to analyze data on one Galaxy instance, and store histories more permanently on another. This is critical for us as we have storage usage limits on the shared machine with the most computational power. Although I am now able to export histories as a file, I cannot import histories. When I choose under history Import From File, I get a message saying the history is importing and will be visible when finished. However, I never see the history. I've tried many combinations with different histories - saving and downloading in the same Galaxy instance, downloading on one instance and importing on the other, saving the file in a different location altogether or using the link provided in export history. I've not been able to import a history from a file. Thanks for any advice. Todd -- *** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *** ___ 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/ ___ 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/
[galaxy-dev] Is there a way to turn of the pretty display for VCF files
Hi,Is there a way to turn of the special pretty print version for VCF files since it is not working correctly?I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is...Where is this pretty printer and how do I turn it off?ThanksThon ___ 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/
Re: [galaxy-dev] Is there a way to turn of the pretty display for VCF files
Hmm. Chrome on OSX looks good to me, please do send over the VCF file and I can take a look. Do you see any javascript errors in the browser console? On May 29, 2012, at 6:31 PM, Anthonius deBoer wrote: Hi Dannon, I could share the VCF file, but I think it is dependent on the browser you use... I used the same file on FireFox on Linux and there it loaded the complete VCF file (Still don't see the Show All option) but on my chrome on Windows 7 it only shows the first 5 lines or so of the genotypes and then nothing...The stuff that IS shown looks correctly formatted etc. it just does not show the rest of the file which it normally does Thon On May 29, 2012, at 03:01 PM, Dannon Baker dannonba...@me.com wrote: There isn't a universe toggle for the tabular display. The VCF datatype inherits the pretty printing from the base tabular datatype, and if you'd like to disable it one way would be to override the display_data method in VCF using the raw Data display_data method. That said, I'd rather just fix your problem. Looking at a few VCF files I have, they look fine. Can you share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: Hi, Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is... Where is this pretty printer and how do I turn it off? Thanks Thon ___ 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/ ___ 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/
[galaxy-dev] starting galaxy server - Paste/egg installation
Hi,
Has there been any change in the way galaxy-dist server is started up? I am
getting following error after running 'run.sh --daemon' command after galaxy
initializes config files from .sample files:
{{{
Initializing community_wsgi.ini from community_wsgi.ini.sample
Initializing datatypes_conf.xml from datatypes_conf.xml.sample
…
...
Initializing tool-data/sequence_index_base.loc from
sequence_index_base.loc.sample
Initializing tool-data/sequence_index_color.loc from
sequence_index_color.loc.sample
Initializing tool-data/sift_db.loc from sift_db.loc.sample
Initializing tool-data/srma_index.loc from srma_index.loc.sample
Initializing tool-data/twobit.loc from twobit.loc.sample
Initializing static/welcome.html from welcome.html.sample
Command 'serve' not known (you may need to run setup.py egg_info)
No commands registered.
Have you installed Paste Script?
(try running python setup.py develop)
}}}
Do I need to install eggs separately using some other script? Any help?
--
Shantanu
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Re: [galaxy-dev] Is there a way to turn of the pretty display for VCF files
What Galaxy revision are you running? Given the new information I'd guess it's an erroneous console.log that was removed in bb7f51fb545d. On May 29, 2012, at 6:49 PM, Anthonius deBoer wrote: Interestingly when I open the Developer Tools in Chrome, my VCF file is actually loading...As soon as I close the developer tool, it stops loading the the page again (and it resumes loading when I re-open the Developer tools...) Really funky... Here's theVCF file...On my computer it only shows up to line 5 112175639 rs121913332 C T 3206.18 PASS AC=3;AF=0.0174;AN=172;COSMIC;DB;DP=15405;Dels=0.00;EFF=DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0502371|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0504915|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0507379|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0512211|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0514164|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0257430|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0457016|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0508376|exon_5_112173250_112181753),TRANSCRIPT(MODIFIERCTC-554D6.1|processed_transcript|NON_CODING|ENST0520401|),UTR_3_PRIME(MODIFIERAPC|protein_coding|CODING|ENST0508624|);GC=45.64;HRun=0;MQ0=0;OND=0.01;set=variant5-variant49-variant10 On May 29, 2012, at 03:39 PM, Dannon Baker dannonba...@me.com wrote: Hmm. Chrome on OSX looks good to me, please do send over the VCF file and I can take a look. Do you see any javascript errors in the browser console? On May 29, 2012, at 6:31 PM, Anthonius deBoer wrote: Hi Dannon, I could share the VCF file, but I think it is dependent on the browser you use... I used the same file on FireFox on Linux and there it loaded the complete VCF file (Still don't see the Show All option) but on my chrome on Windows 7 it only shows the first 5 lines or so of the genotypes and then nothing...The stuff that IS shown looks correctly formatted etc. it just does not show the rest of the file which it normally does Thon On May 29, 2012, at 03:01 PM, Dannon Baker dannonba...@me.com wrote: There isn't a universe toggle for the tabular display. The VCF datatype inherits the pretty printing from the base tabular datatype, and if you'd like to disable it one way would be to override the display_data method in VCF using the raw Data display_data method. That said, I'd rather just fix your problem. Looking at a few VCF files I have, they look fine. Can you share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: Hi, Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is... Where is this pretty printer and how do I turn it off? Thanks Thon ___ 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/ CalledVariants-Select.zip ___ 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/
Re: [galaxy-dev] Is there a way to turn of the pretty display for VCF files
I'm running the latest galaxy central verson that I pulled down today...On May 29, 2012, at 03:59 PM, Dannon Baker dannonba...@me.com wrote:What Galaxy revision are you running? Given the new information I'd guess it's an erroneous console.log that was removed in bb7f51fb545d. On May 29, 2012, at 6:49 PM, Anthonius deBoer wrote: Interestingly when I open the Developer Tools in Chrome, my VCF file is actually loading...As soon as I close the developer tool, it stops loading the the page again (and it resumes loading when I re-open the Developer tools...)Really funky...Here's theVCF file...On my computer it only shows up to line5 112175639 rs121913332 C T 3206.18 PASS AC=3;AF=0.0174;AN=172;COSMIC;DB;DP=15405;Dels=0.00;EFF=DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0502371|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0504915|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0507379|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0512211|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0514164|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0257430|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0457016|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0508376|exon_5_112173250_112181753),TRANSCRIPT(MODIFIERCTC-554D6.1|processed_transcript|NON_CODING|ENST0520401|),UTR_3_PRIME(MODIFIERAPC|protein_coding|CODING|ENST0508624|);GC=45.64;HRun=0;MQ0=0;_OND_=0.01;set=variant5-variant49-variant10 On May 29, 2012, at 03:39 PM, Dannon Baker dannonba...@me.com wrote:Hmm. Chrome on OSX looks good to me, please do send over the VCF file and I can take a look.Do you see any _javascript_ errors in the browser console? On May 29, 2012, at 6:31 PM, Anthonius deBoer wrote: Hi Dannon, I could share the VCF file, but I think it is dependent on the browser you use... I used the same file on FireFox on Linux and there it loaded the complete VCF file (Still don't see the "Show All" option) but on my chrome on Windows 7 it only shows the first 5 lines or so of the genotypes and then nothing...The stuff that IS shown looks correctly formatted etc. it just does not show the rest of the file which it normally does Thon On May 29, 2012, at 03:01 PM, Dannon Baker dannonba...@me.com wrote: There isn't a universe toggle for the tabular display. The VCF datatype inherits the pretty printing from the base tabular datatype, and if you'd like to disable it one way would be to override the display_data method in VCF using the raw Data display_data method. That said, I'd rather just fix your problem. Looking at a few VCF files I have, they look fine. Can you share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: Hi,Is there a way to turn of the special pretty print version for VCF files since it is not working correctly?I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is...Where is this pretty printer and how do I turn it off?ThanksThon___Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at:http://lists.bx.psu.edu/ CalledVariants-Select.zip ___ 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/
