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No action for /admin_toolshed/prepare_for_install
by Pete Schmitt 22 Jul '12

22 Jul '12

I'm trying to install deseq_and_sam2counts from the main toolshed using the admin interface in galaxy. I get the following error: The resource could not be found. No action for /admin_toolshed/prepare_for_install This is on a server that was installed in May 2012. I had performed an 'hg pull -u' on the server and restarted it to see if that would help which it didn't. I was successful installing this tool with a new install of the server on my laptop. I would prefer not to do a fresh install of this main server since it's in use. Is there a manual method to installing tools like this from the toolshed? -- * *

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Is the galaxy main toolshed compatible with local installs of galaxy-dist?
by Ira Cooke 21 Jul '12

21 Jul '12

I was wondering whether the general policy is to keep the toolshed at toolshed.g2.bx.psu.edu compatible with galaxy-dist or galaxy-central. The reason I ask is that I went to install a tool from a production server I'm trying to setup based on galaxy-dist ... but got an error; The resource could not be found. No action for /admin_toolshed/prepare_for_install Searching for this in the source code, I found that it exists in galaxy-central ... but not in galaxy-dist Am I right in guessing that this error is due to toolshed.g2.bx.psu.edu being powered by a recent toolshed version that is incompatible with galaxy-dist? If so, it would be great to get clarification as to whether this is to be expected in future. My personal feeling is that the main toolshed would be much more useful if kept compatible with galaxy-dist. Cheers Ira

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Lost my data on Galaxy
by GEISER Céline 21 Jul '12

21 Jul '12

Hi, When I started Galaxy today I lost more than half of my processed data, weeks of work ;-(. I had a look at the deleted dataset but nothing, If I had erased them erroneously I wouldn't have purge them.... Is it possible that there was a problem with the server? Or do a kind of logfile/history exist to see everything what happened on the account? Thanx and have a nice week-end Céline

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Galaxy July 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Jul '12

21 Jul '12

Galaxy July 20, 2012 Distribution & News Brief *Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20* *Highlights: http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief* * *Freebayes *has moved from the /Galaxy distribution to the Galaxy's Main Tool Shed/ * *EMBOSS* version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing. * *Tool Shed* now also supports specifying the third party tool dependencies to be automatically installed in new repositories * *Admin Genome Indexing* is now in /BETA/. Download, index, and track progress right from the admin UI! * *Improved Error Handling* that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details. * *TopHat2/Bowtie2* latest support includes option to 'report discordant pairs', updated tests, and more preset options. * *Trackster* new parameter space visualization. /Includes BRAND NEW Features!!/ More details coming soon, but give a test drive now. *http://getgalaxy.org* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ec29ce8e27a1 *Thanks for using Galaxy!* We hope to see everyone in /Chicago/ @ *GCC2012*!! The Galaxy Team

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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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