February 2012 - galaxy-dev - lists.galaxyproject.org

Setup questions
by Brami, Daniel 20 Feb '12

20 Feb '12

Hi folks, I am trying to setup a local copy of Galaxy and I am running into a few issues with which I would greatly appreciate some help. 1. I am trying to setup my "built-in" indices for bowtie mapping and I have been following the instructions given at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup very closely. My 'bowtie_indices.loc' file, located in the $GALAXY_DIST/tool-data/ directory has only one entry that is uncommented: #buildname filepath SSURef_108_tax_silva_trunc /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc where the blank spaces are tabs. These instructions differ from those given as comments in the 'bowtie_indices.loc' file, requiring 4 entries. I any case, neither of these formats seem to be working. My file path should be correct: cmd->ls /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/*.ebwt /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc.1.ebwt /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc.2.ebwt /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc.3.ebwt /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc.4.ebwt /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc.rev.1.ebwt /bioinformatics/bio_db/silva_SSURef_108_tax_silva_trunc/bowtie/SSURef_108_tax_silva_trunc.rev.2.ebwt I have re-started my Galaxy server and cleared the cache on my browser and still no success. Should I be modifying any builds.txt file? Any suggestions or am I missing something? 2. Is there planned Galaxy support for bowtie2? 3. I was very impressed by the JGI setup of Galaxy (https://galaxy.jgi-psf.org/) , particularly the NFS file import. How can I implement this on my local copy? Does using this option bypass the 2GB file upload limit of using the GUI? Does the data still go through the browser's POST method? 4. Is there a way to specify the input files for a workflow when running the workflow through the command line? I've only seen methods for monitoring the contents of a folder, not for specifying a pair of input reads (ie: forward / reverse reads from same Lib). Thanks for the advice people! Daniel Brami Synthetic Genomics, Inc. Senior Research Associate, Bioinformatics 11149 North Torrey Pines Road La Jolla, California 92037 Phone: 858.433.2230 Fax: 858.754.2988 DBrami(a)SyntheticGenomics.com<mailto:DBrami@SyntheticGenomics.com> www.SyntheticGenomics.com<http://www.syntheticgenomics.com/>

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BWA empty output and failed alignment
by Praveen Baskaran 20 Feb '12

20 Feb '12

Hi, I have a problem running BWA in my local instance of galaxy. When I try to align the short reads in bwa, sometimes it gives empty file otherwise it throws the following error BWA Version: 0.6.1-r104 The alignment failed. The output file is empty. You may simply have no matches, or there may be an error with your input file or settings But the alignment works fine in command line. Can anyone help me to resolve this issue. Thanks in advance Praveen

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Functional tests
by Frank Sørensen 20 Feb '12

20 Feb '12

Hi Guys, Sorry if this is a stupid question, but in order to find out which external reference files (.loc - list files etc.) we need for our newly installed Galaxy server, and to get an overview of which tools are in working order, I have tried for a couple of days now, to run the script "run_functional_tests.sh". I have copied tool_conf.xml over tool_conf.xml.sample, and I've tried to run all scripts mentioned in http://wiki.g2.bx.psu.edu/Main/Tests/Framework. I have tried to stop the server and run run_functional_tests.sh and all I get is the message saying "Ran 0 tests in 0.000s", and an empty run_functional_tests.html - file. I haven't been able to find any documentation to clarify this matter. Can anyone give me a pointer please? Our Galaxy server is installed using Mercurial on an Ubuntu server. I have written tool-wrappers for some of our own programs, and they all work fine. Regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363

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Using Galaxy as a Framework
by Mikal Ustad 20 Feb '12

20 Feb '12

Hello, I am part of a senior project group at Northern Arizona University. We are interested in adapting Galaxy for a project related to building image processing workflows. The existing system that we are working with uses XML files to make system calls and describe the attributes for each tool, similar to how Galaxy tools work. Galaxy has many features that we were planning on implementing, but there are also quite a few that are not useful to our project. We are wondering if there exists a bare bones build of the Galaxy framework that we could adapt to our specific needs. We appreciate any feedback you may have. Thank You, Mikal Ustad

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cool tool for the week
by Ross 18 Feb '12

18 Feb '12

http://www.biodalliance.org/index.html embeddable - DAS native, but local server bigBed/bigWig files http://www.biodalliance.org/bin.html can be served.

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Re: [galaxy-dev] No Display at UCSC Main link.
by Jennifer Jackson 17 Feb '12

17 Feb '12

Hello Luobin, Thanks for sending the additional information. It sounds as if you are using the default version of: tool-data/shared/ucsc/ucsc_build_sites.txt Adding hg19 to "main" in this file will add the link to the datasets. Hopefully this helps, Best, Jen Galaxy team On 2/17/12 1:58 PM, Luobin Yang wrote: > Hi, Jen, > > I noticed that when I use hg18 or other database builds, the UCSC > display link shows up, but when I use hg19 database builds, there is no > UCSC display link. > > Thanks, > Luobin > > On Wed, Feb 15, 2012 at 11:30 AM, Luobin Yang <yangluob(a)isu.edu > <mailto:yangluob@isu.edu>> wrote: > > Hi, Jen, > > Thanks for your replay. Yes, it's an instance that I installed here > at ISU, not the main instance at PSU. The dataset is BED and the > database is hg19. > > In my universe_wsgi.ini file, I have the following lines: > # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt > ucsc_display_sites = main,test,archaea,ucla > > In my apache configuration file, I added the following: > > <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy#CA-64199e734386081ab1…><Location "/root/display_as"> > <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy#CA-64199e734386081ab1…> Satisfy Any > > Order deny,allow > Deny fromall > Allow fromhgw1.cse.ucsc.edu <http://hgw1.cse.ucsc.edu> > Allow fromhgw2.cse.ucsc.edu <http://hgw2.cse.ucsc.edu> > Allow fromhgw3.cse.ucsc.edu <http://hgw3.cse.ucsc.edu> > Allow fromhgw4.cse.ucsc.edu <http://hgw4.cse.ucsc.edu> > Allow fromhgw5.cse.ucsc.edu <http://hgw5.cse.ucsc.edu> > Allow fromhgw6.cse.ucsc.edu <http://hgw6.cse.ucsc.edu> > Allow fromhgw7.cse.ucsc.edu <http://hgw7.cse.ucsc.edu> > Allow fromhgw8.cse.ucsc.edu <http://hgw8.cse.ucsc.edu> > </Location> > > > One thing I would like to ask you about is for above Apache > configuration, because my Galaxy is served as /galaxy subdirectory > instead of the root directory, do I need to make changed to above > location? for instance, instead of "/root/display_as", use > "/galaxy/root/display_as" ? > > Thanks so much! > Luobin > > > On Tue, Feb 14, 2012 at 10:51 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello again, > > The link is not a Galaxy Main public instance share link, which > would start with: http://main.g2.bx.psu.edu > > Having the datatype as BED and the database as hg19 would (for > all of the cases I can think of) bring up the "View at UCSC" > link, if the instance is set up to have "display at UCSC" > configured. > > So, the root cause of the problem is probably with how this > other instance is set up. If this is not your instance, you will > want to contact the folks running it to see if they have plans > to configure UCSC display. If this is yours, follow the > instructions on this wiki to get set up: > > http://wiki.g2.bx.psu.edu/__Admin/Config/Apache%20Proxy > <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy> > See the section: Display at UCSC > > Hopefully this helps, > > Best, > > Jen > Galaxy team > > > > On 2/14/12 9:26 PM, Luobin Yang wrote: > > Hi, Jen, > > The dataset is BED datatype and the database is hg19. > Actually this > history contains the same steps as those in Galaxy101 tutorial. > > I created the link for the history and here it is: > > XXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > So basically I do not see an option called "Display at UCSC > Main", but > it has two other options, "View in GeneTrack" and "Display > at Ensemble > Current" > > Thanks, > Luobin > > On Tue, Feb 14, 2012 at 9:35 PM, Jennifer Jackson > <jen(a)bx.psu.edu <mailto:jen@bx.psu.edu> > <mailto:jen@bx.psu.edu <mailto:jen@bx.psu.edu>>> wrote: > > Hi Luobin, > > To display at UCSC, the datatype has to be a UCSC > display type and > the database has to be a UCSC genome browser. Often, > small changes > can be made to tune a dataset to help it fit into these > requirements. Other times, a dataset will need to be > transformed > into another type or it can't be viewed at all because > the genome is > not available at UCSC. > > You should try to modify these attributes yourself > first. Common > UCSC datatypes from Galaxy are: BED, bigBED, BAM. For > the list of > UCSC known datatypes, see: > http://genome.ucsc.edu/FAQ/____FAQformat.html > <http://genome.ucsc.edu/FAQ/__FAQformat.html> > <http://genome.ucsc.edu/FAQ/__FAQformat.html > <http://genome.ucsc.edu/FAQ/FAQformat.html>>. > > > Known databases would be any that you also can find at: > http://genome.ucsc.edu as full genome assemblies. The short > label > used at UCSC should match the database assignment at > Galaxy. For > example, the most recent human would be "hg19" at both. > > If you are still stuck and would like to send me a > shared history > link, I can provide feedback about how to modify (if > possible) to > view at UCSC. Use "Options -> Share or Publish", > generate the link, > and email this link directly back to me. Be sure to > include the > dataset #, so that I know which in your history you want > to view at > UCSC. > > Best, > > Jen > Galaxy team > > > On 2/14/12 11:50 AM, Luobin Yang wrote: > > Hi, > > I have a local instance of Galaxy, but I found there > is no > "Display at > UCSC Main" link for some datasets that can be viewed > in GeneTrack or > displayed by Ensemble, what has been wrong? > > Thanks, > Luobin > > > > _________________________________________________________________ > > 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/ > > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/____Support > <http://galaxyproject.org/wiki/__Support> > <http://galaxyproject.org/__wiki/Support > <http://galaxyproject.org/wiki/Support>> > > > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/__Support > <http://galaxyproject.org/wiki/Support> > > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Switching Torque>PBSpro: qsub error 111 (cannot connect to server)
by Louise-Amélie Schmitt 17 Feb '12

17 Feb '12

Hello, We want to move Galaxy's jobs from our small TORQUE local install to a big cluster running PBS Pro. In the universe_wsgi.ini, I changed the cluster address as follows: default_cluster_job_runner = pbs:/// to: default_cluster_job_runner = pbs://sub-master/clng_new/ where sub-master is the name of the machine and clng_new is the queue. However, I get an error when trying to run any job: galaxy.jobs.runners.pbs ERROR 2012-01-16 11:10:00,894 Connection to PBS server for submit failed: 111: Could not find a text for this error, uhhh This corresponds to the qsub error 111 (Cannot connect to specified server host) which is, for some reason, caught by pbs_python as an error of its own (111 not corresponding to any pbs_python error code, hence the face-plant-message). Our guess is that we might need to re-scramble the pbs_python egg with PBS pro's libraries, is that correct? If it's the case, what do we have to set as LIBTORQUE_DIR? Thanks, L-A

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transferring sample datasets stuck in 'In queue' status
by Luobin Yang 17 Feb '12

17 Feb '12

Hi all, I configured Sample Tracking System in Galaxy to transfer datasets from a sequencer to data libraries, however, after I selected the datasets to be transferred on the sequencer and clicked "Transfer" button, the transfer status has been "in queue" forever. I didn't find any error message in galaxy_listener.log, however, I found the following error message in data_transfer.log: 2012-02-16 19:39:01,221 - datatx_3623 - Error. <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>405 Method Not Allowed</title> </head><body> <h1>Method Not Allowed</h1> <p>The requested method PUT is not allowed for the URL /api/samples/1e8ab44153008be8.</p> <hr> <address>Apache/2.2.14 (Ubuntu) Server at xxx.xxx.xxx.xxx Port 80</address> </body></html> Any idea what went wrong? Thanks, Luobin

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Galaxy and Cluster options
by Tanguy LE CARROUR 17 Feb '12

17 Feb '12

Hi! Is there a way to specify parameters for the job submission on the cluster from the tool configuration file? Let's say I want tool A to be submitted with "-pe smp 8" but tool B submitted with "-l mem_free=500". Is it already supported? I could not find it in the wiki. ... or do I have to start digging in the code and try to implement it?! ^_^' Best regards, Tanguy

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Re: [galaxy-dev] [galaxy-user] FTP in local galaxy Instance
by Dannon Baker 17 Feb '12

17 Feb '12

Hi Paula, There's one more FTP option in your universe_wsgi.ini, directly below the one you set: # This should be the hostname of your FTP server, which will be provided to # users in the help text. # ftp_upload_site = None Additionally, I've copied this over to galaxy-dev, which is more useful for local instances and galaxy/tool development. -Dannon On Feb 16, 2012, at 1:25 PM, Paula R. Kuser-Falcao wrote: > Hi, > > We have set up a local galaxy instance and the settings in the universe file to be able to > upload FTPed files. > > The settings in the universe_wsgi.ini seem correct and are : >> >> >> # This should point to a directory containing subdirectories matching >> users' >> # email addresses, where Galaxy will look for files. >> ftp_upload_dir = /var/www/galaxy-dist/ftp >> > > I have also set ftp_upload_site. > > But when the users sign into galaxy they cannot view their file in the get data -> from files > on my computer. > > When I use the Galaxy server at main.g2.bx.psu.edu I see the ftp files option no problems. > > Can you suggest something else I should be doing to have this feature to work? > > Thanks, > > Paula Kuser-Falcao > > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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