- galaxy-dev - lists.galaxyproject.org

nglims/removing multiplexing
by Lee Katz 03 Jul '13

03 Jul '13

Hi, I would like to remove the "multiplexed" menu from the nglims sample information form. How would I do that? In our lab, we don't want submitters making their own libraries since they might accidentally use the same barcodes or somehow mess up others' libraries. We want to remove that option altogether. Actually along the same lines, we would like to remove all "services needed" check boxes too and simply have all of the data entry on one page. Thank you for your help. -- Lee Katz, Ph.D.

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Galaxy + google analytics?
by Steve.Mcmahon＠csiro.au 03 Jul '13

03 Jul '13

Has anyone hooked Galaxy up to Google analytics? We get great reporting from the Galaxy reports interface but we don't get number of connections and some other things that Google analytics would give us. :) Sent from my iPad

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Debugging the execution errors of the Python tools
by Hyungro Lee 02 Jul '13

02 Jul '13

Hi, I am new here and trying to use the Galaxy toolkit for my project on the Windows Azure cloud environment. The thing is I got errors when I tested the 101 example on my local machine, so I looked 'stderr' via View details and it only showed 'Killed' which is not much information to do debugging. I looked web logs and found out the execution is : 'python /home/.../galaxy-dist/tools/new_operations/gops_join.py /home/.../galaxy-dist/database/files/000/dataset_1.dat /home/.../galaxy-dist/database/files/000/dataset_2.dat /home/.../galaxy-dist/database/files/000/dataset_3.dat -1 1,2,3,6 -2 1,2,3,6 -m 1 -f none' which is about joining two datasets. I believe the input data sets and the parameters are okay since I tested it on the galaxy public server. To get more debugging information, I tried to run the job on shell but got same results, Killed. I was wondering is there a way that I can get more information about the execution of the tool other than looking into the source code line by line? That might be helpful to figure out what I am doing wrong for this test. Thanks, Hyungro

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error while writing to pdf in python
by vijayalakshmi 02 Jul '13

02 Jul '13

Hi, I am writing a python script that will take in two parameters (an input file and an ouput file name) , plot a graph and output it to the filename specified. PYTHON SCRIPT #!/usr/bin/python import sys import numpy as np import matplotlib.pyplot as plt input_file = sys.argv[1] output_file = sys.argv[2] mydata = np.loadtxt(input_file) plt.figure(1) plt.plot(mydata[:,0],mydata[:,1],label = "Feature"); plt.plot(mydata[:,0],mydata[:,2], label = "Variance"); plt.xlabel('Distance from feature(bp)'); plt.ylabel('Score'); plt.title(sys.argv[1]); plt.legend(loc="best") plt.savefig(output_file) SAMPLE COMMAND : <command interpreter="python"> plot.py $ref_filename $out_file1 </command> <inputs> <param name="ref_filename" type="data" format="gen,txt,gtf,bed" label="Reference/Coordination file" help="Choose a reference file"/> </inputs> <outputs> <data name="out_file1" format="pdf" /> </outputs> When I run this, I am getting the following error. File "/panfs/panfs.ccr.buffalo.edu/projects/mjbuck/galaxy/CistromeAP/tools/ArchTex/plot.py", line 22, in <module> plt.savefig(output_file) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/pyplot.py", line 345, in savefig return fig.savefig(*args, **kwargs) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/figure.py", line 990, in savefig self.canvas.print_figure(*args, **kwargs) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/backend_bases.py", line 1399, in print_figure '%s.' % (format, ', '.join(formats))) ValueError: Format "dat" is not supported. Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz. I don't know how to make the script extract ".pdf" from the ".dat" Thanks, VJ.

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Re: [galaxy-dev] [Galaxy-gcc2013] Strange behaviour with galaxy history
by Ambrose Andongabo (RRes-Roth) 02 Jul '13

02 Jul '13

Dear Carl, The javascript console displayed no errors. Below is the output of hg summary [root@vnc galaxy-dist]# hg summary not trusting file /home/data/galaxy-python/galaxy-dist/.hg/hgrc from untrusted user andongab, group csys not trusting file /home/data/galaxy-python/galaxy-dist/.hg/hgrc from untrusted user andongab, group csys parent: 10002:9d42f1e32efb For user impersonation, fully log the admin out prior to assuming user persona to avoid any history/session corruption. branch: stable commit: 241 unknown (clean) update: (current) As for the galaxy log, there is no error 149.155.13.62 - - [02/Jul/2013:15:40:33 +0100] "GET /api/histories/2d89e36a8c9b5508 HTTP/1.1" 200 - "http://vnc:8080/history" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0" 149.155.13.62 - - [02/Jul/2013:15:40:37 +0100] "GET /api/histories/2d89e36a8c9b5508 HTTP/1.1" 200 - "http://vnc:8080/history" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0" 149.155.13.62 - - [02/Jul/2013:15:40:42 +0100] "GET /api/histories/2d89e36a8c9b5508 HTTP/1.1" 200 - "http://vnc:8080/history" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0" I hope this helps Thanks Ambrose From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: 02 July 2013 15:33 To: Ambrose Andongabo (RRes-Roth) Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [Galaxy-gcc2013] Strange behaviour with galaxy history Hi, Ambrose A couple of places to start: Did the javascript console (in Firefox: Tools->Web Developer->Web Console) display any errors when you reloaded the failing saved history page? What does is the output of 'hg summary' when run in a terminal from your Galaxy root directory? I believe you mentioned there were no 'ERROR' messages in the Galaxy log; is this correct? Thanks for the report. (I'm moving this to the galaxy-dev mailing list). Carl On Tue, Jul 2, 2013 at 3:50 PM, Ambrose Andongabo (RRes-Roth) <Ambrose.Andongabo(a)rothamsted.ac.uk<mailto:Ambrose.Andongabo@rothamsted.ac.uk>> wrote: Dear All, I updated my local galaxy instance yesterday and all my users cannot access their saved histories. When they click on saved histories all they get is an empty page. Checking the database, all the histories are there. I cleared the browser cache as many suggested but no luck yet. Any ideas of what can be done?? Thanks Ambrose -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. _______________________________________________ Galaxy-gcc2013 mailing list Galaxy-gcc2013(a)lists.bx.psu.edu<mailto:Galaxy-gcc2013@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-gcc2013 -- This message has been scanned for viruses and dangerous content by MailScanner<http://www.mailscanner.info/>, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning.

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Re: [galaxy-dev] [Galaxy-gcc2013] Strange behaviour with galaxy history
by Carl Eberhard 02 Jul '13

02 Jul '13

Hi, Ambrose A couple of places to start: Did the javascript console (in Firefox: Tools->Web Developer->Web Console) display any errors when you reloaded the failing saved history page? What does is the output of 'hg summary' when run in a terminal from your Galaxy root directory? I believe you mentioned there were no 'ERROR' messages in the Galaxy log; is this correct? Thanks for the report. (I'm moving this to the galaxy-dev mailing list). Carl On Tue, Jul 2, 2013 at 3:50 PM, Ambrose Andongabo (RRes-Roth) < Ambrose.Andongabo(a)rothamsted.ac.uk> wrote: > Dear All, > > I updated my local galaxy instance yesterday and all my users cannot > access their saved histories. When they click on saved histories all they > get is an empty page. Checking the database, all the histories are there. I > cleared the browser cache as many suggested but no luck yet. Any ideas of > what can be done?? > > > > Thanks > > Ambrose > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and we believe > but do not warrant that this e-mail and any attachments > thereto do not contain any viruses. However, you are fully > responsible for performing any virus scanning. > > > _______________________________________________ > Galaxy-gcc2013 mailing list > Galaxy-gcc2013(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-gcc2013 >

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Multiple output files do not appear in history
by Christoph Malisi 02 Jul '13

02 Jul '13

Hey, I'm writing a XML for a tool that produces a number of output files. As the number is not known before the tool is run, I used the strategy outlined here: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_… First, I tried my tool definition in a galaxy instance in a virtual machine to not interrupt our production instance (we have a local instance set up). Here, everything worked fine. When trying the same code in our production galaxy instance, it didn't: Regardless of how many output files were produced, only one appears in the history. (the first one, corresponding to "output1" in the references wiki entry). When looking at the temp directory provided to the tool by galaxy ("$__new_file_dir__" in the wiki, it always points to "galaxy-dist/database/tmp/"), the additional output files have been created by my tool and are named correctly (e.g. primary_123_output2_visible_fastq, primary_123_output3_visible_fastq, …) Both instances are new, based on release_2013.06.03. Is there any setting in galaxy somewhere that could prevent this from working? Thanks for your help Chris PS: I wrote a little python script that just creates multiple output files, and the discrepancy between the two instances is reproducible. Here is the code for the python script and the corresponding XML: ####### import subprocess import argparse import os def main(): parser = argparse.ArgumentParser() parser.add_argument('-i', type=int) parser.add_argument('output1') parser.add_argument('output1_id') parser.add_argument('out_dir') args = parser.parse_args() print 'Wrapper arguments:', args with open(args.output1, 'w') as f: f.write('output1') for i in range(2, args.i+1): name = 'output%i'%i file_type = 'text' fname = '%s_%s_%s_%s_%s' % ('primary', args.output1_id, name, 'visible', file_type) with open(os.path.join(args.out_dir, fname), 'w') as f: f.write('output%i'%i) if __name__ == "__main__": main() ############################ ########################### <tool name="MultiOutTest" id="multiouttest"> <description>Multiple Outputs test</description> <command interpreter="python"> multiout.py -i $how_many $output1 $output1.id $__new_file_path__ </command> <inputs> <param name="how_many" type="integer" value="2" label="How many output files?"/> </inputs> <outputs> <data name="output1" format="txt"/> </outputs> <help> This is some help text. </help> </tool> ################################# -- Dr. Christoph Malisi Computomics GmbH & Co. KG Sand 14 · 72076 Tübingen · Germany http://computomics.com

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Error running tophat2 in Galaxy
by Sachit Adhikari 02 Jul '13

02 Jul '13

I am getting this error: Error in tophat: [2013-02-13 20:46:41] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-02-13 20:46:41] Checking for Bowtie Bowtie version: 2.0.6.0 [2013-02-13 20:46:41] Checking for Samtools Samtools version: 0.1.18.0 [2013-02-13 20:46:41] Checking for Bowtie index files [2013-02-13 20:46:41] Checking for reference FASTA file Warning: Could not find FASTA file /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa [2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index Executing: /usr/bin/bowtie2-inspect /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > ./tophat_out/tmp/genome.fa [2013-02-13 20:48:51] Generating SAM header for /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome format: fastq quality scale: phred33 (default) [2013-02-13 20:49:23] Preparing reads left reads: min. length=34, max. length=34, 2 kept reads (0 discarded) Warning: you have only one segment per read. If the read length is greater than or equal to 45bp, we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments [2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2 [2013-02-13 20:49:56] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. Warning: junction database is empty! [2013-02-13 20:51:18] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done What's wrong?

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Upload files to data library
by Lionel Guy 01 Jul '13

01 Jul '13

Hi! I'm trying to upload multiple files a data library on my local instance of Galaxy. I've looked at the tutorial on the Galaxy wiki (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles) where it's said that there are four options to upload files, available by clicking the arrow at the top of the page one gets to when clicking on the add dataset button. However, although the tutorial shows the text "Create new data library datasets" with an arrow next to it, the page I get to when clicking on "Add datasets" shows "Upload files to a data library" with no arrow. I thus cannot add files otherwise than by uploading files one by one. Did I miss something? Am I doing anything wrong? I'm using: $ hg tip changeset: 10003:b4a373d86c51 tag: tip parent: 10001:471484ff8be6 Thanks for your help! Lionel Uppsala University

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Insert link in page editor
by Ted Goldstein 01 Jul '13

01 Jul '13

I want to make the page editor more useful. This may be more a WYM editor question than a Galaxy question. But since Galaxy has its own enhanced WYM editor, I figure I would start here. I was trying to use the galaxy page WYM editor today and I inserted a link (see image below). The behavior seems to put a wym guid as the text. I would have expected the title text prose from the dialogue box. Can anyone comment on this? Why insert a weird non-user friendly WYM stamp guid? Thanks, Ted

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