June 2010 - galaxy-user - lists.galaxyproject.org

file formats in workflows
by Paul Webster 04 Jun '10

04 Jun '10

Hi, Was impressed by the Worflow screencasts but when I converted my history to a workflow it failed. This is because some of the tools output tabular data, but some downstream tools require interval format input and therefore fail. When I made the history I manually changed the file format and nominated the fields for chr,start,end,strand, but this is lost in the workflow. Obvious ideas: * Use a tabular-to-interval tool - I looked but can't find one * Only used tools which output interval format - a less desirable solution. e.g. I can't figure out how to filter out duplicate codons in my gene-BED-to-codon-BED file except using the statistics->count function which outputs tabular. Has anyone worked out how to change formats within a workflow? regards, Paul

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Re: [galaxy-user] Question on Illumina read data upload to Galaxy
by Anton Nekrutenko 02 Jun '10

02 Jun '10

Jeff: Unfortunately there is no straightforward way to do this in your context. Can you put the files somewhere else on the web and use URL upload? anton On Jun 2, 2010, at 12:05 PM, Whyte, Jeffrey wrote: > Dear Dr. Nekrutenko, > > First of all, I would like to thank you and congratulate you and > your colleagues on providing such an excellent collaborative > resource with the Galaxy web application. The interface and > tutorials are very professional, and the amount of time and effort > put into the project must have been immense. > > I had a question that I posted to the SeqAnswers Bioinformatics > Forum regarding upload of NGS files to the Galaxy server, but have > received no response. I was hoping you could point me in the right > direction. > > I would like to upload Illumina FASTQ files to Galaxy via the FTP > URL method described on the Galaxy website. However, our University > Bioinformatics facility states: "FTP connections from remote systems > are not allowed. Remote file transfer connections must be initiated > using a secure FTP (SFTP) client program that authenticates to the > server using SSH version 2". > > Is there any way that I can upload the file from our Linux system > (e.g. use FTP "PUT" to transfer the file to Galaxy)? Uploading the > file directly from my desktop (OS X) takes hours, and I was hoping > that the FTP protocol would speed this process. > > Thank you in advance for any advice or assistance you can provide. > > Sincerely, > Jeff Whyte > > ----- > Jeffrey J. Whyte, PhD > Department of Biomedical Sciences > University of Missouri-Columbia > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Installing galaxy with sge
by Mariette 02 Jun '10

02 Jun '10

Hi everyone, I installed galaxy on our system and it worked just fine until I tryed to settled it up to make it run on our cluster. So I edited the universe_wsgi.ini file as following: # Comma-separated list of job runners to start. local is always started. If # left commented, no jobs will be run on the cluster, even if a cluster URL is # explicitly defined in the [galaxy:tool_runners] section below. The runners # currently available are 'pbs' and 'sge'. start_job_runners = sge # The URL for the default runner to use when a tool doesn't explicity define a # runner below. For help on the cluster URL format, see the ClusteringGalaxy # Wiki. Leave commented if not using a cluster job runner. default_cluster_job_runner = sge://INRA_CLC/wflowq//-R y -l h_vmem=8G -l mem=8G I also did the egg thing like this : SGE_ROOT=/SGE/n1ge62 python2.5 scripts/scramble.py DRMAA_python This line looks like it worked out. Then when starting the engine, I'm catching this error : Traceback (most recent call last): File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/app.py", line 69, in __init__ self.job_manager = jobs.JobManager( self ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/__init__.py", line 40, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/__init__.py", line 777, in __init__ self.job_runners[runner_name] = runners.sge.SGEJobRunner( app ) File "/usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/runners/sge.py", line 83, in __init__ self.ds.init( self.default_cell ) File "build/bdist.linux-x86_64/egg/DRMAA.py", line 186, in init errParse(eno, estr) File "build/bdist.linux-x86_64/egg/DRMAA.py", line 167, in errParse else: raise _errindex[errno-_errMin](errstring) InvalidArgumentError: The input value for an argument is invalid. Exception DRMAA.NoActiveSessionError: NoActiveSessionError('',) in <bound method Session.__del__ of <DRMAA.Session object at 0x104e2bd0>> ignored I'm guessing someting weird is happening with the DRMAA eggs, so I edited the /usr/local/bioinfo/src/galaxy_dist/lib/galaxy/jobs/runners/sge.py to figure out if the module is well loaded and sounds like it is ! So I'm kind of lost ... do you have any idea on what is going on ? One other weird think is that I had to unset some tools from the tool_conf.xml when starting with the sge parameters, what hadn't to be done whitout sge, does it sounds normal to you ? thanks, Jerome

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Intersect BED data
by Steve Taylor 02 Jun '10

02 Jun '10

Hi, I recently did an intersect on two *identical* BED format feature sets exported from UCSC in Galaxy and got no results (see attached png). I tried it on our local install and remote install and both gave the same answer. Please can someone advise why this doesn't work? Many thanks for any help, Steve

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SNPs and conservation
by Paul Webster 02 Jun '10

02 Jun '10

Hi, I'm trying to investigate conservation in SNPs using Galaxy, but running into a few "issues" so I'm probably not doing this the best way. Here is what I did in Galaxy: (1) Get some high heterozygosity missense SNPs from UCSC for chr21 (2) Get all Genes from UCSC for chr21 (3) Split the genes into codons using the "Gene BED to Codon BED expander" (4) Join the SNPs(1) to the Codons(2) using {Operate on genomic intervals}->Join (5) Create a multiple alignment for the codons which had SNPs using {Fetch Alignments}->{Extract MAF blocks} Some problems I found were: * The SNP file contains 149 regions but when joined to the Codons there are 311 items in the output. I was expecting one joined record per SNP. * The joined file contains many duplicate SNPs and missing SNPs * MAF blocks are all in same orientation but about half the codons should be in the reverse direction Can anyone offer advice? Thanks, Paul ****************************************************************** sample output ****************************************************************** (1) SNPs (149 records) chr21 15436474 15436475 rs3859679 missense TAT,TTT, Y,F, chr21 15481364 15481365 rs7278737 missense GAC,GAA, D,E, chr21 15516947 15516948 rs2822432 missense GAA,AAA, E,K, (2) Genes (901 records) chr21 9690070 9690100 uc002zkg.1 0 + 9690070 9690070 0 1 30, 0, chr21 9711934 9769223 uc011abu.1 0 + 9711934 9711934 0 10 104,31,70,82,29,73,71,164,195,379, 0,34186,36895,40899,43769,43889,49915,54029,55562,56910, chr21 9907192 9908487 uc010gqn.1 0 - 9907192 9907192 0 2 982,210, 0,1085, (3) Codons (327,371 records) chr21 9908330 9908333 uc002zka.1 0 - chr21 9908333 9908336 uc002zka.1 0 - chr21 9908336 9908339 uc002zka.1 0 - (4) Join (311 records) chr21 15481364 15481365 rs7278737 missense GAC,GAA, D,E, chr21 15481364 15481367 uc002yjm.2 0 - GAC chr21 15516947 15516948 rs2822432 missense GAA,AAA, E,K, chr21 15516945 15516948 uc002yjm.2 0 - GAA chr21 15596771 15596772 rs409782 missense TTG,GTG, L,V, chr21 15596771 15596774 uc002yjn.3 0 + TTG

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