July 2012 - galaxy-dev - lists.galaxyproject.org

bed files - The uploaded binary file contains inappropriate content
by Robert Chase 20 Jul '12

20 Jul '12

Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. -Rob

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Problem installing repositories from local tool shed: JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)
by Jon Manning 20 Jul '12

20 Jul '12

Hi all, I'm new to Galaxy- so hello, and excuse me while I get to grips with all the conventions! I've successfully got my local Galaxy (galaxy-central) install set up and working correctly, as well as a local toolshed. I've also linked the two with a line in tool_sheds_conf.xml. But I'm getting the following problem when I try to install tools from the local toolshed (either ones I tried to make myself, or ones I downloaded from the Galaxy public toolshed). The following appears when I click 'install to local Galaxy': URL: http://www.my.domain/galaxy/admin_toolshed/prepare_for_install?tool_shed_ur… File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/var/www/galaxy_home/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/var/www/galaxy_home/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 978 in prepare_for_install repo_information_dict = from_json_string( raw_text ) File '/var/www/galaxy_home/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/__init__.py', line 384 in loads File '/var/www/galaxy_home/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 402 in decode File '/var/www/galaxy_home/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg/simplejson/decoder.py', line 420 in raw_decode JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) The following error sometimes (not always, but that may be due to my use of Varnish) pops up in my apache logs when the above appears, could this be linked? File does not exist: /var/www/galaxy_home/galaxy-central/static/scripts/packed/modernizr.js, referer: http://www.my.domain/galaxy/admin Pertinent configuration details: * Galaxy and the toolshed proxied from Apache on another machine. * A Cosign-based authentication system is in place, so 'use_remote_user = True' in both Galaxy and the toolshed. * Galaxy's home dir is at /var/www/galaxy_home for consistency with other things I run. All input appreciated. Thanks, Jon -- Dr Jonathan Manning Bioinformatics Team Centre for Cardiovascular Science University of Edinburgh Queens Medical Research Institute 47 Little France Crescent Edinburgh EH16 4TJ United Kingdom T: +44 131 242 6700 F: +44 131 242 6782 E: jmanning(a)staffmail.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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building a full trinity workflow from assembly through analysis
by Brian Haas 20 Jul '12

20 Jul '12

Greetings all, I'm trying to build out a Galaxy workflow to support trinity rna-seq de novo assembly and all the various downstream analyses. For the initial trinity de novo assembly, I took Jeremy's initial workflow and tweaked it to work with the latest release - and submitted it to the galaxy tool shed. So, step 1 is done. But... here's what I'm ultimately trying to accomplish: Given fastq files for a number of different samples {A,B,C} 1. merge {A,B,C,...} => MERGED.fq 2. run Trinity based on MERGED.fq to generate Trinity.fasta (existing workflow does this already) 3. align the original {A,B,C,...} separately to Trinity.fasta using bowtie 4. for each alignment, perform abundance estimation 5. combine results from each abundance estimation into a matrix file 6. run some Bioconductor tools to analyze differential expression There are some complexities here, such as not knowing ahead of time how many different samples are to be processed - so this needs to be determined dynamically, which impacts the overall complexity of the total workflow. Is this possible in Galaxy, and if so, are there examples I can work from? There are a whole bunch of other add-ons I'd like to include beyond the above, but I figure that if the above is doable, then the rest should be equally doable. Many thanks! -- -- Brian J. Haas Manager, Genome Annotation and Analysis, Research and Development The Broad Institute http://broad.mit.edu/~bhaas

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samtools pileup deprecated
by Bossers, Alex 20 Jul '12

20 Jul '12

Hi All, Maybe I missed it on the list here, but it seems that for samtools the pileup command has been deprecated without backward compatibility from the more recent samtools packages... http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html Did anyone rewrite some of the samtools tool wrappers for this....? I am currently testing whether the Bam->pileup command can be easily changed in the sam_pileup.py script. But some functionality has gone and some additional is there. It seems I am up-to-date with the latest wrappers in the galaxy_dist repository. Any pointers to recent wrappers would be welcomed. Alex

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Tool added / pb with output file
by Sarah Maman 20 Jul '12

20 Jul '12

Hello, I have added a tool in my local instance to map BAM files on reference genome fasta file thanks to BWA. This tool runs, and the output file generated in database/files/000 is correct (not empty and good data inside) but the output listed in the history panel of Galaxy interface , is empty. Could you please help me ? Here is my xml file: <tool id="BWA_aln_sampe" name=" BWA with BAM files"> <description>BWA mapping BAM files on reference genome fasta file</description> <command interpreter="perl">bwa_aln_sampe.pl $input1 $input2 $output1 </command> <inputs> <param format="fasta" name="input1" type="data" label="Reference genome from your history - fasta file"/> <param format="bam" name="input2" type="data" label="Bam file"/> </inputs> <outputs> <data format="bam" name="output1" /> </outputs> <help> This tool map BAM files on a reference genome. </help> </tool> Here is my perl file : #!/usr/bin/perl -w use strict; use File::Basename; my $input_ref_genome = $ARGV[0]; my $input_bam = $ARGV[1]; my $output_bam = $ARGV[2]; my $input_dir=dirname($input_bam); my $input_basename=basename($input_bam,'.bam'); my $input_bamsorted="$input_dir/${input_basename}-sorted"; #Ouverture des fichiers entrants open (IN, "<$input_ref_genome") or die "Cannot open $input_ref_genome !"; open (IN, "<$input_bam") or die "Cannot open $input_bam !"; #Indexation du genome de reference #system("bwa index $input_ref_genome >> ./bwa.log 2>&1"); #Tri par nom du bam entrant pour travailler sur des donnees pairees system("samtools sort -n $input_bam $input_bamsorted >> ./samtools.log 2>&1"); #Alignement des donnees pairees uniquement system("bwa aln $input_ref_genome -b1 ${input_bamsorted}.bam > ${input_bamsorted}-1.sai >> ./bwaaln.log 2>&1"); system("bwa aln $input_ref_genome -b2 ${input_bamsorted}.bam > ${input_bamsorted}-2.sai >> ./bwaaln.log 2>&1"); #bwa sampe system("bwa sampe $input_ref_genome ${input_bamsorted}-1.sai ${input_bamsorted}-2.sai ${input_bamsorted}.bam ${input_bamsorted}.bam | samtools view -bS - > $output_bam >> ./bwa.log 2>&1"); close( IN ); close( IN ); Thanks in advance, Sarah

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output file
by 張詩婷 19 Jul '12

19 Jul '12

Hi, After execution, my tool created many files in a directory , how can I to find this directory? command: bash mytool.sh $input

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Get job working directory
by Roberto Di Lauro 19 Jul '12

19 Jul '12

Hi all. Is there a way to get the job working directory or the job id from the implementation of "exec_before_job" hook? This hook function produces a file and I would like to store it in a job working directory. Thanks. Roberto

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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows
by Sascha Kastens 19 Jul '12

19 Jul '12

Hi! Yeah, it seems that there is now way to request the API key automatically. One simple apporach would be an extra text input field where the user has to enter his or her API key. In my use case it will be better to use a file for mapping $__user_id__ -> api_key. We run Galaxy only locally, so it would not be a security issue at all. Cheers, Sascha

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Automatic Tools installation error
by Sabbir Joy 19 Jul '12

19 Jul '12

Dear all, I am facing a uncertain problem,which i didn't face it before. Just sometimes before i have installed a new galaxy instances ,so when i logged in as an admin, i am facing a tools installation problem .i have attached the screen-shot. beside this , i turned on this line in universe.wsgi.ini tool_config_file = tool_conf.xml,shed_tool_conf.xml, still facing this problem. regards sabbirjoy

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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows
by Sascha Kastens 19 Jul '12

19 Jul '12

Hi Geert, thanks for your reply. Unfortunately it is not feasible for us to use a script outside Galaxy. As long as no official feature for Galaxy is released I will work on a script which will execute workflows via the API and add this script as a tool into Galaxy. Cheers, Sascha Original message: Hi, In case you?d be interested: we use a script that creates interlaced data of paired end data. We run this outside galaxy on groups of samples ordered in directories at once. We then import the interlaced data into galaxy, enabling batch workflow. The first step of the workflow is a deinterlacing of the datafiles. The script is available here: http://geertvandeweyer.zymichost.com/index.php?page=read&id=27 Best Regards, Geert On 07/18/2012 02:38 PM, Sascha Kastens wrote: > > Hi Dev-Team, > > are you planning or maybe working on an update which enables the > > possiblilty to run workflows in batch mode with paired end data? > > Cheers, > > Sascha > > > > ___________________________________________________________ > 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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