January 2014 - galaxy-dev - lists.galaxyproject.org

February 2014 Galaxy Update Newsletter
by Dave Clements 31 Jan '14

31 Jan '14

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bowtie2 toolshed installation
by Alexander Kurze 31 Jan '14

31 Jan '14

Hi there, I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057… ) I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't... Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2. Is there a way to add bowtie2 manually? Best wishes, Alex

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filter tag in output, multiple criteria
by Geert Vandeweyer 31 Jan '14

31 Jan '14

Hi, I'm looking for the correct syntax to achieve the following: <data type="data" format="txt" name="loh" label="${tool.name} result on ${on_string} (loh) " > <filter>outtype == "0" || outttype == "2" </filter> </data> <data type="data" format="txt" name="cnv" label="${tool.name} result on ${on_string} (loh) " > <filter>outtype == "1" || outttype == "2" </filter> </data> I tried the above, with and without parentheses, but it creates the second dataset also when outtype == 0. Is this type of dual filtering possible? Best, Geert -- 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/in/geertvandeweyer

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bias correction in cufflinks
by Malik, Shivani 30 Jan '14

30 Jan '14

Hi, I want to use the bias correction parameter in cufflinks but cannot figure out how to get the multifasta file need for it. Can someone help. Thanks Shivani

1 0

Galaxy local toolshed - issue hg pushing
by Eric Rasche 30 Jan '14

30 Jan '14

Devs, I'm having issues with a local toolshed I'm playing around with. I turned on use_remote = True (since we have that working on our primary galaxy instance). Web access to the tool shed, cloning, and pulling work fine. However, I'm getting "abort: authorization failed" when trying to "hg push". Our webserver is seeing it OK, all the authorizations look good (first one fails with 401, so hg requests creds from me and sends those, gets 200) X - - [30/Jan/2014:18:28:28 -0600] "GET /toolshed/repos/esr/genemarks_tools?cmd=capabilities HTTP/1.1" 401 5213 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:30 -0600] "GET /toolshed/repos/esr/genemarks_tools?cmd=capabilities HTTP/1.1" 200 4893 "-" "mercurial/proto-1.0" Everything past here is where the fun starts... those are 401s for perfectly good credentials... X - - [30/Jan/2014:18:28:30 -0600] "GET /toolshed/repos/esr/genemarks_tools?cmd=batch HTTP/1.1" 401 730 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:30 -0600] "GET /toolshed/repos/esr/genemarks_tools?cmd=batch HTTP/1.1" 200 4797 "-" "mercurial/proto-1.0" X - - [30/Jan/2014:18:28:30 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 730 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:30 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 5175 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:33 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 5175 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:33 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 5175 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:33 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 5175 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:33 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 5175 "-" "mercurial/proto-1.0" X - esr@DOMAIN [30/Jan/2014:18:28:33 -0600] "POST /toolshed/repos/esr/genemarks_tools?cmd=unbundle HTTP/1.1" 401 5175 "-" "mercurial/proto-1.0" And galaxy _seems_ to be seeing it OK 165.91.51.54 - - [30/Jan/2014:18:28:30 -0500] "GET /toolshed/repos/esr/genemarks_tools?cmd=capabilities HTTP/1.1" 200 130 "-" "mercurial/proto-1.0" 165.91.51.54 - - [30/Jan/2014:18:28:30 -0500] "GET /toolshed/repos/esr/genemarks_tools?cmd=batch HTTP/1.1" 200 43 "-" "mercurial/proto-1.0" however, on my end I'm seeing: esr:~/Projects/genemarks_tools$ hg push pushing to https://esr@fqdn/toolshed/repos/esr/genemarks_tools http authorization required realm: Galaxy Toolshed user: esr password: searching for changes http authorization required realm: hgweb in the tool shed user: esr password: abort: authorization failed The 200 I get in response to cmd=batch isn't actually a 200. Running the same GET from the command line (GET /toolshed/repos/esr/genemarks_tools?cmd=batch) or browsing via the web I see Galaxy was unable to successfully complete your request URL: https://example.org/toolshed/repos/esr/genemarks_tools?cmd=batch Module galaxy.web.framework.middleware.error:*149* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>app_iter *=* self*.*application*(*environ*,* sr_checker*)*| Module paste.debug.prints:*106* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>environ*,* self*.*app*)*| Module paste.wsgilib:*543* in |intercept_output| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>app_iter *=* application*(*environ*,* replacement_start_response*)*| Module paste.recursive:*84* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.webapps.tool_shed.framework.middleware.remoteuser:*74* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* self*.*app*(* environ*,* start_response *)*| Module paste.httpexceptions:*633* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.web.framework.base:*132* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* self*.*handle_request*(* environ*,* start_response *)*| Module galaxy.web.framework.base:*199* in |handle_request| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* body*(* environ*,* start_response *)*| Module mercurial.hgweb.request165.91.51.54:*146* in |run_wsgi| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* application*(*env*,* respond*)*| Module mercurial.hgweb.hgwebdir_mod:*147* in |__call__| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* self*.*run_wsgi*(*req*)*| Module mercurial.hgweb.hgwebdir_mod:*205* in |run_wsgi| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* hgweb*(*repo*)**.*run_wsgi*(*req*)*| Module mercurial.hgweb.hgweb_mod:*127* in |run_wsgi| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>*return* protocol*.*call*(*self*.*repo*,* req*,* cmd*)*| Module mercurial.hgweb.protocol:*76* in |call| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>rsp *=* wireproto*.*dispatch*(*repo*,* p*,* cmd*)*| Module mercurial.wireproto:*347* in |dispatch| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>args *=* proto*.*getargs*(*spec*)*| Module mercurial.hgweb.protocol:*32* in |getargs| |>> <https://geiger.tamu.edu/toolshed/repos/esr/genemarks_tools?cmd=batch#>data*[*k*]* *=* knownargs*[*k*]**[**0**]*| *KeyError: 'cmds'* Additionally, when I browse via the web/curl, I see the following in the tool_shed_webapp.log: X - - [30/Jan/2014:19:05:33 -0500] "GET /toolshed/repos/esr/genemarks_tools?cmd=batch HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:26.0) Gecko/20100101 Firefox/26.0" Error - <type 'exceptions.KeyError'>: 'cmds' Any ideas? Cheers, Eric Rasche -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 <tel:4046922048> esr(a)tamu.edu <mailto:esr@tamu.edu>

1 0

GATK2
by Briand, Sheldon 30 Jan '14

30 Jan '14

Hi, I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here. I've run into the following error: ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does not exist. I see via much googling that this error is due to a user input problem. I've tried pointing the gatk2_picard_index.loc file in tool-data to the proper data files: hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa where the following files exist: hg19.dict hg19.fa hg19.fa.fai I'm using a torque setup. A bam file is being used as input. After much trial and error I've been unable to figure out what I'm missing. None of the solutions on google apply to my situation. Has anyone else run into this configuration problem and solved it? Thanks, -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand(a)ssc-spc.gc.ca

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Toolbox filtering question
by Lukasse, Pieter 30 Jan '14

30 Jan '14

Hi, I would like specify a filter based on a role. Does someone know how to do this? I already have an example on how to do this based on user id (found at https://wiki.galaxyproject.org/UserDefinedToolboxFilters#For_Administrators) but now I would like to filter out menu items in case users don't have a specific role. Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

2 2

object_store_conf.xml route users to different storage
by Eric Kuyt 30 Jan '14

30 Jan '14

Hi all, At gcc2013 at the storage workshop I think I heard about a feature in galaxy, where different users could be assigned to a specific object store. But I can't find any documentation on this subject. Is this possible and how do I implement this? Thanks, -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

1 0

questions about mapping tools 'bowtie2'
by wang haifang 30 Jan '14

30 Jan '14

Hi, I am going to analyze one ChIP-seq data using "Gaxlaxy", the data upload, and format converting goes well, then I use "bowtie2" to map the reads, there is no result come out for quite a long time, the jobs is always "waiting to run". Could you tell me how can I fix this? PS:my account: wanghf(a)picb.ac.cn -- Sincerely Wang Haifang CAS-MPG partner institute for Computational Biology Shanghai institutes for Biological Sciences wanghf810501(a)gmail.com wanghf(a)picb.ac.cn

1 0

RNA-seq
by Karla Fernández Cano 29 Jan '14

29 Jan '14

Hi, My name is Karla Fernández a student of a University in Nuevo Leon in Monterrey, Mexico (UANL). The reason for this mail is because i'm going to work with differential gene expression of the yeast Pichia pastoris and i'd seen that the complete genome and annotations of this yeast are absent in programs like bowtie, tophat and cufflinks, I wondered if it might be possible to upload the genome and annotations of these yeast for my DGE. Thank you so much QBP. Karla Fernández Cano

1 0