July 2013 - galaxy-dev - lists.galaxyproject.org

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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Strange Issue with Data Libraries
by Patel, Viren 01 Jul '13

01 Jul '13

Hello. After creating a data library and clicking on the 'Manage Data Libraries' menu to show the list of libraries, clicking on a data library name results in an "Unable to connect" message in Firefox, no action in Safari, and an "Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection." when using Chrome. However, in all browsers, copying the link and pasting it into a new window works fine (the datasets/folders of the library are displayed and I can work with them normally). There are no messages in the Galaxy logs, web server logs, or system logs. Any insights to resolve this? Thanks. ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Strange Issue with Data Library
by Patel, Viren 01 Jul '13

01 Jul '13

Hello. After creating a data library and clicking on the 'Manage Data Libraries' menu to show the list of libraries, clicking on a data library name results in an "Unable to connect" message in Firefox, no action in Safari, and an "Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection." when using Chrome. However, in all browsers, copying the link and pasting it into a new window works fine (the datasets/folders of the library are displayed and I can work with them normally). There are no messages in the Galaxy logs, web server logs, or system logs. Any insights to resolve this? Thanks. ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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fastQ groomer waiting to run problem
by Xu, Ye 01 Jul '13

01 Jul '13

Hi there, I am using Galaxy at BioCloud Central. I have successfully transferred total 30GB fastQ data from amazon S3 to galaxy. I tried to run fastQ groomer for each samples. But it said the job is waiting to run. I have waited a couple days and the job is still waiting. I called AWS, they told me my cluster working fine. So I don't know why the job can't start. Thank you so much. Best, Ye Xu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Patch in reference to trello card#968
by Eric Enns 01 Jul '13

01 Jul '13

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