May 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance
by Jayant Khopale 31 May '11

31 May '11

Hi Vipin, I was successfully able to integrate the tools in my local version of Galaxy. Thanks a lot for your time and help. The issue that I could isolate was probably due to the incorrect integration of the Postgresql database. On Mon, May 30, 2011 at 2:41 AM, Vipin TS <vipin.ts(a)gmail.com> wrote: > > >> >> >>> The log file comes out to be clean. However I have 2 questions - >>> >> >> When you start your instance I am sure apache log will say something for >> ex: clicking on the page, selecting tool etc. I am sure about that. >> >> >>> >>> 1. Which version are you using to run your test instance? >>> >> >> The recent one, but it is quite sure that the tool integration in quite >> stable from past couple of months. >> >> >>> 2. Did you make any changes to your Python execution environment for >>> Galaxy? >>> >>> >> From the error it seems that it is not problem with Python environment >> set-up. >> >> >>> Please let me know. >>> >>> >> >> > How is going with your Galaxy tool integration, I was away for the last > couple of days. > Hope things are worked at your end. > > -- JAYANT KHOPALE

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Is dynamic associated information per dataset possible?
by Duddy, John 30 May '11

30 May '11

We'd like to be able to associate fixed things (project, Sample, sequencer used) with user's FASTQ files, and we'd also like to allow users to associate dynamic, site-specific stuff with the sequencing run. Currently, users track their runs using a CSV sample sheet, and often they add columns to that sample sheet for their own information. Is it possible to associate that information with the FASTQ file when it is placed in Galaxy? I know about metadata, but the supported fields look like they are fixed in the code. I was hoping for a solution where the users do not need to modify the Galaxy code to pull this off. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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thanks for the conference; presentations availbale?
by Martin Senger 30 May '11

30 May '11

I really enjoyed the recent conference. Many thanks for the splendid logistics and, of course, the content. I wonder if the slides presented there will be available for downloading perhaps? Cheers, Martin -- Martin Senger email: martin.senger@gmail.com,martin.senger@kaust.edu.sa skype: martinsenger

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semi-colons converted to X in config file?
by Jon Sorenson 29 May '11

29 May '11

I suspect I've run into a rare XML entity/Cheetah conversion bug. I have a parameter definition like <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> I also am creating a configfile using <configfile name="iniFile"> ... paramSchedule=${schedule} ... </configfile> The file that gets created has ... paramSchedule=6,3,75X6,3,75X5,3,75X5,3,75X6,2,75X6,2,75X5,2,75X5,2,75 ... i.e. the ';' character gets converted to X. I suspect that this is an XML parsing issue (trying to interpret ';' as marking an entity resolution?) but the default value get displayed correctly in the Galaxy UI so it might not be so simple as this. I can't see how Cheetah is converting ';' to 'X' but maybe that's it. I'm planning on hacking around this, but wanted to post to the list to see if anyone else has seen this or has quick recommendations. Jon

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Filter data and cut column bugs
by Peter Cock 27 May '11

27 May '11

Hi all, I filled the following bugs 2 weeks ago, with patches: https://bitbucket.org/galaxy/galaxy-central/issue/537/ Filter data on any column tool casts unused columns https://bitbucket.org/galaxy/galaxy-central/issue/536/ Filter data on any column tools shows nonsense % vs total on stdout https://bitbucket.org/galaxy/galaxy-central/issue/535/ Filter data on any column tool complains about hash comment lines https://bitbucket.org/galaxy/galaxy-central/issue/534/ Cut column tool messes up # header lines I'm sure the team has been busier than usual with the run up to the Galaxy Community Conference (hopefully I'll see you all tomorrow night - fingers crossed the ash from the Grimsvotn volcano doesn't cause too much trouble)... However, for future reference would it help if I emailed the list in parallel with filing bugs? None of these issues individually are overly complicated, and the sooner they get looked at the more likely it is my patches will still apply cleanly. Thanks, Peter

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Workflows and unknown number of output datasets
by Louise-Amélie Schmitt 27 May '11

27 May '11

Hi everyone First let me thank all the Team Galaxy, the conference was really great. Kanwei asked me to send the tool I told him about. It's one of these tools for which you can't know the exact number of output datasets before tool run. Here are the files. It's really simple actually, but it would be nice if I could integrate it in workflows without it having to be the final step. Would it even be possible? And please ignore the idiotic comments in the files, I was really tired that day. Cheers, L-A

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Re: [galaxy-dev] stdout and stderr
by Peter Cock 27 May '11

27 May '11

On Fri, May 27, 2011 at 3:27 AM, shashi shekhar <meshashi29(a)gmail.com> wrote: > if i am using pbs . in this i am getting stderror and stdout . then how can > i handle such type of problem How does the tool you are wrapping signal an error? Does it write to stderr and/or does it give a non-zero return code? The BLAST+ wrapper script looks for a non-zero return code, since BLAST+ will write harmless warnings to stderr which should not be treated as an error. Note the changes suggested on issue 325 have have not been made yet (in part because supporting PBS nicely would be hard). Peter

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GATK integration
by Jan Haas 27 May '11

27 May '11

Hey, I know, the GATK-tools is considered to be in alpha status, but maybe someone can help me. First, is there a documentation on which dependencies where to put (just to confirm I've done it correctly) ? Second, when I run the unified genotyper, I get the following error: [Wed May 25 15:57:04 CEST 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/var/folders/gr/grLYUw45FFS4KKMXzK5R6++++TI/-Tmp-/tmp7m3sg0/gatk_input.fasta OUTPUT=/var/folders/gr/grLYUw45FFS4KKMXzK5R6++++TI/-Tmp-/tmp7m3sg0/dict6511818973877179087.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 TMP_DIR=/var/folders/gr/grLYUw45FFS4KKMXzK5R6++++TI/-Tmp-/ngs2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed May 25 15:57:04 CEST 2011] net.sf.picard.sam.CreateSequenceDictionary done. Runtime.totalMemory()=129957888 Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:178) at net.sf.picard.reference.IndexedFastaSequenceFile.getSequence(IndexedFastaSequenceFile.java:157) at net.sf.picard.reference.IndexedFastaSequenceFile.nextSequence(IndexedFastaSequenceFile.java:234) at net.sf.picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:133) at net.sf.picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:113) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) at org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSource.(ReferenceDataSource.java:131) at org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine.openReferenceSequenceFile(AbstractGenomeAnalysisEngine.java:577) at org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine.initializeDataSources(AbstractGenomeAnalysisEngine.java:318) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:90) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:97) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:244) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) I assume, changing the java heap size will solve the problem. But how can I do it in galaxy ? Thanks for your help! Jan

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stdout and stderr
by shashi shekhar 26 May '11

26 May '11

Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar

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The powers of Cheetah, how?
by Kempenaar, M (med) 26 May '11

26 May '11

Hi list, I've been working on a single Galaxy tool for a while now, and I'm running into all sorts of difficulties that can probably all be fixed using Cheetah. However I've been trying several ways of utilizing the (enormous) powers of Cheetah but so far I'm not successful. I'll try to ask my questions as clear as possible, please let me know if anything is unclear. In my tool I use the following input parameter: ----------------------- <param name="report_options" type="select" multiple="True" display="checkboxes"> <option value="overview">phyla distribution</option> <option value="phyladend">phyla dendograms</option> <option value="heatmap">heatmap</option> <option value="dendogram">dendogram</option> <option value="pca">principal component analysis</option> <option value="mds">multi dimensional scaling</option> </param> ----------------------- Each of these options corresponds to a function in my R script, thus I want to do an if-else if-else to execute these functions that the user selected (note that multiple="True"). Now the problem is, I also use R Sweave (sweaving R output (text/graphics) into LaTeX) to generate a nice looking PDF report, and since that's not a 'real' programming/ scripting language, I can't for instance split the string (as I used to do in R) and check for the boxes a user selected, so my questions are: I planned on using Cheetah to include sections of Sweave LaTeX code for each box checked by the user, perfectly doable with an #if-#elif you'd think, however since the $report_options contains a comma-separated single string, I would need to split (or use regular expressions) to be able to do such an #if-#elif like: #if "heatmap" in $report_options.split(",") results in: "NotFound: cannot find 'split' while searching for 'split'" ----------------------- Questions: Q: How can I use this string with Cheetah, or is the low-level Python object (i.e. a list) also available (that is used to generate this string)? Q: You can use a <filter> for the <output> parameters, which doesn't work with $report_options in this case, so how to use the <filter> with 'multiple_select="True"'? Q: While trying out some Cheetah functionality (as explained in the Cheetah manual), I've came across a number of 'things' in the Cheetah documentation that aren't supported in Galaxy tool XML files. Is there some documentation available showing what is possible and what isn't? Q: Followup from previous question, where within the sections of my tool XML file can I actually use Cheetah? This of course has to do with the order in which a tool is executed. ----------------------- Any help or pointers / examples are greatly appreciated! Some links: - Cheetah Manual: http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html _ Excellent post about Cheetah on the mailing list: http://gmod.827538.n3.nabble.com/Bitten-by-a-Cheetah-long-td2760688.html Regards, Marcel ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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