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Jobs remain in queue until restart
by Thon Deboer 14 Aug '13

14 Aug '13

Hi, I have noticed that from time to time, the job queue seems to be "stuck" and can only be unstuck by restarting galaxy. The jobs seem to be in the queue state and the python job handler processes are hardly ticking over and the cluster is empty. When I restart, the startup procedure realizes all jobs are in the a "new state" and it then assigns a jobhandler after which the jobs start fine.. Any ideas? Thon P.S I am using the june version of galaxy and I DO set limits on my users in job_conf.xml as so: (Maybe it is related? Before it went into dormant mode, this user had started lots of jobs and may have hit the limit, but I assumed this limit was the number of running jobs at one time, right?) <?xml version="1.0"?> <job_conf> <plugins workers="4">  <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="8"/> <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="2"/> </plugins> <handlers default="handlers">  <handler id="handler0" tags="handlers"/> <handler id="handler1" tags="handlers"/> <handler id="handler2" tags="handlers"/> <handler id="handler3" tags="handlers"/>  </handlers> <destinations default="regularjobs">  <destination id="local" runner="local"/> <destination id="regularjobs" runner="drmaa" tags="cluster">  <param id="nativeSpecification">-V -q long.q -pe smp 1</param> </destination> <destination id="longjobs" runner="drmaa" tags="cluster,long_jobs">  <param id="nativeSpecification">-V -q long.q -pe smp 1</param> </destination> <destination id="shortjobs" runner="drmaa" tags="cluster,short_jobs">  <param id="nativeSpecification">-V -q short.q -pe smp 1</param> </destination> <destination id="multicorejobs4" runner="drmaa" tags="cluster,multicore_jobs">  <param id="nativeSpecification">-V -q long.q -pe smp 4</param> </destination>  <destination id="dynamic" runner="dynamic">  <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> <tools>  <tool id="bwa_wrapper" destination="multicorejobs4"/> </tools> <limits>  </limits> </job_conf>

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Galaxy database check script
by graham etherington (TSL) 14 Aug '13

14 Aug '13

Hi, I've been getting some errors on our local Galaxy instance which haven't been solved by updating to the latest code. Some of them involve sql-type errors. My sys-admin informed me that "There are a couple of SQL errors being reported, i.e. text attempting to be inserted into an integer field within the sql statements." I'm also getting 'NoneType' object has no attribute 'x' errors [where 'x' can be a number of different attributes]. Are there any scripts in Galaxy that I can run to test the database. I'm wondering if there's some sort of corruption with the database. Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

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Duplicated entries in "Manage installed tool shed repositories" table
by Peter Cock 14 Aug '13

14 Aug '13

Hi Greg, I'm seeing something strange on a system running the August stable release of galaxy-dist, $ sudo -u galaxy hg head changeset: 10393:d05bf67aefa6 branch: stable tag: tip user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Aug 12 11:55:41 2013 -0400 summary: Added tag release_2013.08.12 for changeset 1ae95b3aa98d changeset: 10390:009088d5e76f user: Ross Lazarus <ross.lazarus(a)gmail.com> date: Sat Aug 10 11:28:28 2013 +1000 summary: Patch for missing options in FromDataTableOutputActionOption when these are used in an output filter 1. Run Galaxy 2. Log in as an administrator 3. Click on Admin (top menu) 4. Click on "Manage installed tool shed repositories" (left menu) 5. Observe duplicate entries: Names of repositories for which updates are available are highlighted in yellow. Description Owner Revision Installation Status Tool shed Galaxy wrappers for Emboss version 5.0.0 tools devteam c159a6ded912 Installed toolshed.g2.bx.psu.edu Galaxy applicable data formats used by Emboss tools. devteam a89163f31369 Installed toolshed.g2.bx.psu.edu Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. bgruening b1ad88bbc5fa Installed toolshed.g2.bx.psu.edu Gene calling with glimmer and a trainingset of know genes. bgruening 22bfc027a718 Installed toolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 1.61 of the biopython package. biopython b482933a6de5 Installed toolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc c85236cd100d Installed testtoolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc 9ff9bfdcd04f New testtoolshed.g2.bx.psu.edu NCBI BLAST+ 2.2.26 (binaries only) iuc 0e536576294c New testtoolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 2.4 of the freetype font library. iuc 8761091302c4 Installed toolshed.g2.bx.psu.edu Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package iuc 74c21f9bdc39 Installed toolshed.g2.bx.psu.edu As you can see I have been trying the NCBI BLAST+ package from the TEST tool shed, http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Why are there these extra entries (older revisions) labelled with an "Installation Status" of "New"? Are they relics from failed installation attempts? Thanks, Peter

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Fwd: Map with BWA results in correpted SAM file
by Moritz Juchler 14 Aug '13

14 Aug '13

Hey Folks, Is there really nobody that can help Geert and me? Thats quite important to me right now. This is obviously not something specific to me, as Geert has the exact same error. I meanwhile tried to replace the id with "1" but it still doesnt work. Best Moritz ______________________________ Von: galaxy-dev-bounces(a)lists.bx.psu.eduIm Auftrag vonGeert Vandeweyer Gesendet: Donnerstag, 8. August 2013 17:18:59 (UTC+01:00) Amsterdam, Berlin, Bern, Rom, Stockholm, Wien An: galaxy-dev(a)lists.bx.psu.edu Betreff: Re: [galaxy-dev] Map with BWA results in correpted SAM file to add on this : we have similar issues (sam-to-bam conversion fails with similar errors). it seems to be related to the BWA output getting messed up, with (part of) columns missing or duplicated on some lines. I have not found a systematic pattern in the errors, they seem to happen rather random. On 08/08/2013 05:06 PM, Moritz Juchler wrote: Dear Galaxy Community, I have a local instance and installed 0.5.9-r16 BWA and the toolshed wrapper. The mapping is successful. I then use the Filter Sam Tool on the sam file from the alignment, but it spits out this error: Dataset 26: Filter SAM on data 24 Tool execution generated the following error message: Traceback (most recent call last): File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148, in <module> if __name__ == "__main__": main() File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 137, in main flags = int( fields[flag_col] ) ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433' I have the same workflow online and did the exact same steps on the same fastq files. Is there anything I am missing? Is there any information I can provide to answer this question? Best Moritz ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- 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<mailto:geert.vandeweyer@ua.ac.be> http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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outputs label attribute
by Jun Fan 14 Aug '13

14 Aug '13

Dear all, I have managed to use something like <outputs> <data format="fasta" name="output" label="#echo os.path.splitext (str ($input.name))[0]#-ORF.fasta"/> </outputs> to display the wanted label for the dataset in the history. However when I applied the same code to other tool wrappers, some weird things happened: the wrapper can still be loaded in the web page, but when I click the execute button to submit the job, nothing happened except the web browser giving the status "wait for localhost". I cannot think of any reason for that. The main difference I can think of between the successful wrapper and the failed ones is that in the failed ones I have to do some file manipulations as galaxy always stores its dataset with the file suffix .dat which is not acceptable in the tool, e.g. proteowizard. I have to rename it with the correct suffix and move the final result to the output file. Additional related questions: 1. How to display the selected value of a conditional element in the label? $conditional.value? 2. How to display different strings according to the conditional selection? Similar to command element to use #if #elsif #end if? 3. When using <data name="output" format="csv"> <change_format> <when input="type" value="html" format="html"/> </change_format> </data>, could I use label attribute in the data and when elements? Look forward to your kind answers. Many thanks in advance. Best regards! Jun

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Tool params passed to python dynamic job runner
by Ganote, Carrie L 14 Aug '13

14 Aug '13

Hi List, I've run into a frustration recently with passing values to the dynamic job runner from a tool. Here's what's going on: in ncbi_blastn_wrapper.xml: <param name="pathToModule" type="hidden" value="/abs/path/to/module" /> ... in dynamic_runner.py: ... def blastn_wrapper(job): incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] ) modulePath = incoming["pathToModule"] modulePath.replace("\"", "").strip() dummy = '/abs/path/to/module' equals = (modulePath == dummy) log.debug( '\n~%s~\n~%s~\nsame? %s' % (mypath, dummy, equals) ) ... log: ~"/abs/path/to/module"~ ~/abs/path/to/module~ same? False I have no idea why these "" are persisting, or if that is even the problem. I can't find the modulePath when using os.path.exists(modulePath). What I want to do is optionally (user checks a box) run another python script that splits up the blast queries into a bunch of jobs and submits each job separately - and I was just going to import this other script using sys.append(modulePath) in some poor attempt to keep the system cleaner. If this is a problem with my understanding of python, please enlighten me - if there are other tools that pass around paths or if there's another way to do this in less hacky way, I'm open to advice. Thanks! Carrie Ganote

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adding reference genome
by Vijay Kumar 14 Aug '13

14 Aug '13

Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u

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ENA galaxy import link broken?
by Andrew Warren 13 Aug '13

13 Aug '13

Hello, I am trying to use the ENA galaxy import feature. This involves going to the analyze menu in galaxy and clicking the link 'EBI SRA' which is encoded as http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=https%3A//main.g2.bx.psu.ed… This does not seem to be working at present. I manage a Galaxy site that uses a similar setup encoded as (also doesn't work) http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=http%3A//rnaseq.pathogenpor… I sent an email off to ENA but haven't got a response. Any ideas? Thanks for any help, Andrew Warren

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Cloudman could not determine the version of Tophat and cufflinks.
by Anto Praveen Rajkumar Rajamani 13 Aug '13

13 Aug '13

Hello, Along with the Tophat (could not determine version: http://dev.list.galaxyproject.org/Problems-with-Tophat-amp-uploading-files-…) problem in my cloudman, I experience a similar problem with Cufflinks. I uploaded a trial BAM file and ran cufflinks 0.0.6. The run failed and I got a message that "Could not determine the version of Cufflinks". When I tried to report the bug using the green bug icon, I get a message "Mail is not configured to report this bug". I updated my Galaxy to http://bit.ly/galaxy20130812 and restarted my instance. My instance is on, but I am unable to analyse my data. Where do I go wrong? Kindly help me to solve this problem. Thank you. Best wishes, Anto

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Urgent Help Required.....Fastq file
by Vengurlekar, Priyanka (NIH/NCI) [C] 13 Aug '13

13 Aug '13

Hello, I am trying to upload this following file on galaxy and den use the barcode splitter....but it does not upload the file at all. I followed you videos to upload the data too and i am using browse to upload this fastq file. would like you to try to upload and let me know if it works if not why doesnt it work. I tried two other files too. and they too cannot be uploaded it turns red in color immediately. can you tell me why as this is very important.Thanking you, Sincerely, Priyanka.V

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