January 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Output files using format="input"
by Peter 06 Jan '11

06 Jan '11

On Wed, Dec 15, 2010 at 9:08 PM, James Taylor <james(a)jamestaylor.org> wrote: > > Excerpts from Peter's message of Wed Dec 15 17:18:05 +0000 2010: >> >> Is there some undocumented trick like format="input:paramname" >> where you can specify the input parameter name? > > No, but that is a great idea. > :-) In the meantime, I think I can workaround this for a short list of known formats using <change_format>, akin to the way the wrapper fastq/fastq_combiner.xml maps the FASTA and QUAL input file formats to the FASTQ output variant. Peter

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Upload files from filesystem paths for non admin users
by Jean-Baptiste Denis 05 Jan '11

05 Jan '11

Hello everybody, I'm running a fresh galaxy-dist installation (changeset 4640:8729d2e29b02) on a Centos 5.5 distribution. I'm using LDAP authentication through Apache. Here is the situation. As a galaxy admin, i've created a "new data library" called "TP" through the admin interface. I've another user, called "foobar" which belongs to a group called "TP Admin" which is associated to the role "TP Admin". I've edited the permissions of the "TP" library to only associate "TP Admin" role to "add library item". No other entry is associated with any role. The "foobar" user logs into galaxy and go to "Shared Data/Data libraries". He chooses "TP" and click on "Add datasets". The problem is that the option "Upload files from filesystem paths" appears in the scrolling "upload option" list even if "foobar" is not a galaxy admin. This means that he can virtually access any file on the filesystem. The comments in the "universe_wsgi.ini" mention "Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to." which seems ok for Galaxy admins, but it looks like this is also the case for any galaxy user. Any advice on this behaviour? Maybe i misunderstood something. Regards, Jean-Baptiste Denis

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Software Carpentry 4.0 course seats still available; register by January 7
by Dave Clements 05 Jan '11

05 Jan '11

Hello all, This is only tangentially related to Galaxy, but given the course's great reputation and it's Python emphasis, I thought I would forward it on to the Galaxy community. Thanks, Dave C. From: Greg Wilson <gvwilson(a)cs.utoronto.ca> Date: January 2, 2011 8:10:54 AM EST Subject: I realize it's hard to do this over the holidays... Hi everyone, Our next online run kicks off a week from Monday (Jan 10) --- of the 105 people who said they'd sign up, only 79 have filled in the full reg. form (I think the prerequisite programming exercise scared many of them off). That means we have room for approximately 20 more students --- it's free, but we will ask them to commit to 3-4 hours/week for 10-12 weeks. Topics will include: * program design (using Python) * version control * testing and test-driven development * basic data crunching using SQL and regular expressions * an intro to object-oriented programming (again using Python) * matrix computation (NumPy, MATLAB, etc.) * the Unix shell and Make (if there's time and demand) http://software-carpentry.org/4_0/ has a list of lecture topics from the fall run; http://software-carpentry.org/about/three-minute-pitch/ has a quick pitch, and http://software-carpentry.org/about/testimonials/ has feedback from alumni. If you have colleagues or grad students who'd like to take the course, please have them contact me directly as soon as possible --- we're going to close off registration on Jan 7. Thanks, and best wishes for 2011, Greg -- http://galaxyproject.org

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XML files for displaying BAM/BigWig in GBrowse from Galaxy
by Stephen Taylor 04 Jan '11

04 Jan '11

Hi, Does anybody have working bigwig.xml and bam.xml files for Galaxy to allow viewing data in GBrowse (to be added to display_applications/gbrowse/) ? I would be really grateful if these could be posted somewhere and perhaps incorporated into future releases of Galaxy. Many Thanks and Happy New Year :-), Steve

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genetrack behind https
by Ry4an Brase 03 Jan '11

03 Jan '11

I'm trying to get genetrack working for bed data and when clicking on the 'Genetrack' link for a bed format dataset I get a 500 Internal Server Error django exception from http://genetrack.g2.bx.psu.edu saying 'Unable to validate key!'. Example on our staging server: http://genetrack.g2.bx.psu.edu/galaxy?filename=2f70726f6a6563742f67616c6178… The GALAXY_URL I'm sending it decodes to: http://dbw-galaxy.msi.umn.edu/tool_runner?tool_id=predict2genetrack which redirects (302) to: https://dbw-galaxy.msi.umn.edu/tool_runner?tool_id=predict2genetrack However, I don't see a request for either in the Apache log. Can the genetrack.g2.bx.psu.edu server be used for other galaxy installations as can the UCSC visualizer and I'm running afoul of my redirect and/or https setup, or should I have figured out that I need my own genetrack server from https://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplication… ? Thanks, -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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using drmaa-python
by David Hoover 03 Jan '11

03 Jan '11

Hi, I've gotten drmaa-python working for PBS Pro. Is there a resource somewhere that describes how to configure a tool for queues, node properties, etc., in the [galaxy:tool_runners] section? David Hoover Helix Systems Staff http://helix.nih.gov

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Searching in Galaxy drop down lists
by Peter 03 Jan '11

03 Jan '11

Hello all, I was finding it frustrating to use the genome select drop down in Galaxy. On the public instance there are about 800 entries (mostly bacteria), and for many organisms there are multiple entries (e.g. five releases for human). I was thinking some kind of heirachy would be useful here until I realised how well the search works. I'm now facing the same problem with other long drop down select parameters (e.g. BLAST+ databases). Can the same nice search feature be enabled in any select parameter via the tool's XML definition? Thanks, Peter

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Creating a script via a script
by Victor Ruotti 03 Jan '11

03 Jan '11

Hi, I wanted to see if there is a way to automatically create a library folder within a data library via a script. Either a bash shell or perl program. Basically a way for us to automatically add a data set based a system path and have this ready for within galaxy. Thanks in advance. Victor

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Re: [galaxy-dev] [galaxy-user] Error in running Cuffcompare
by Jeremy Goecks 03 Jan '11

03 Jan '11

It turns out this problem may also arise from a mismatch between the version of Cuffcompare that Galaxy expects and the version of Cuffcompare actually present on the system. Specifically, up to galaxy-central changeset 4789:d258d5bf9843, Galaxy expects Cuffcompare version 0.9.2 or lower. If you were using Cuffcompare version 0.9.3, you would get this error. As of galaxy-central changeset 4780:8273a8243639, Galaxy expects and works correctly with Cufflinks/Cuffcompare version 0.9.3 You can get this changeset by pulling directly from our in-development repository at: http://bitbucket.org/galaxy/galaxy-central or by waiting for our next stable release, which should hopefully be out later this week. Thanks, J. On Dec 24, 2010, at 11:09 PM, Nate Coraor wrote: > Hi, > > Because your cuffcompare tool runs on a cluster, please ensure that > $TEMP on your Galaxy server is set to a directory which is shared across > the cluster. By default temporary files will be created in /tmp, and > this directory is local to each system. > > --nate > > vasu punj wrote: >> I get the error message run Cuff compare with Cufflinks- GTF file and Ensembl file downloaded to Galaxy. To download Ensembl file Is used following procedure: >> Get Data --> UCSC Main >> select clade/genome/assembly >> for group, use 'Genes and Gene Prediction Tracks' >> for track, use Ensembl >> for table, choose the default (enGene) >> region: genome >> output format: GTF >> >> The error message is:Error in cuffcompare: >> [Errno 2] No such file or directory: '/tmp/9935868.hpc-pbs.usc.edu/tmpGXnESn/input1.tmap' >> Begin PBS Prologue Thu Dec 23 16:29:09 PST 2010 >> Job ID: 9935868.hpc-pbs.usc.edu >> Username: ramjan >> Group: hsc-ar >> Name: 84_cuffcompare_ramjan(a)usc.edu >> Queue: laird >> Shared Access: yes >> Nodes: hpc2712 >> TMPDIR: /tmp/9935868.hpc-pbs.usc.edu >> End PBS Prologue Thu Dec 23 16:29:09 PST 2010 >> ---------------------------------------- >> Warning: no access to tty (Bad file descriptor). >> Thus no job control in this shell. >> ---------------------------------------- >> Begin PBS Epilogue Thu Dec 23 16:29:21 PST 2010 >> Job ID: 9935868.hpc-pbs.usc.edu >> Username: ramjan >> Group: hsc-ar >> Job Name: 84_cuffcompare_ramjan(a)usc.edu >> Session: 29712 >> Limits: neednodes=1:ppn=8,nodes=1:ppn=8,walltime=100:00:00 >> Resources: cput=00:00:09,mem=62512kb,vmem=288372kb,walltime=00:00:12 >> Queue: laird >> End PBS Epilogue Thu Dec 23 16:29:21 PST 2010 >> ---------------------------------------- >> >> >> >> > >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user J.

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displaying data at UCSC via Galaxy using https
by Stephen Taylor 03 Jan '11

03 Jan '11

Hi, I am trying to display some data in the main public UCSC genome browser via our local Galaxy instance (based on http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications… and http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy) I removed the strip_https="True" form the bigwig.xml in display_applications/ucsc, because we only support https on our server and it seems UCSC does support retrieving data over https. When I try to view a bigWig file in Galaxy (that I have tested works via https URL directly in UCSC): "xxxx.bigwig is not a chromosome id r-tree index file" in a UCSC panel at the UCSC site. or "udc couldn't read 4 bytes from xxxx.bigwig, did read 0" (where xxxx = https URL) If I then add in my machine to the apache conf and try and see download xxxx.bigwig via a web browser I get: "Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. Please contact your local Galaxy administrator." I was assuming setting deny/allow would negate the need for a password on these files when connected to by approved servers, but perhaps I am doing something wrong here? Another question I have is should I use <Location "/display_as"> (as per http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy) or <Location "/display_application"> since their doesn't seem to be display_as in the URL. I use the same deny/allow for both to be on the safe side: <Location "/display_application"> Satisfy Any Order Deny,Allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> <Location "/display_as"> Satisfy Any Order Deny,Allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> Any ideas would be much appreciated! Thanks in advance, Steve

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