- galaxy-dev - lists.galaxyproject.org

How to add to add hg16 index into the build-in index / reference gnome list?
by Sachit Adhikari 12 Dec '12

12 Dec '12

How do I add hg16 into the build-in index?

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Questions about Install GATK on local instance
by ygong＠cpdr.org 12 Dec '12

12 Dec '12

Hi, all, I'm installing GATK on galaxy local instance now and I have some questions may need your help. I downloaded the GATK2 from GATK website htt http://www.broadinstitute.org/gatk/download . the link is http://www.broadinstitute.org/gatk/auth?package=GATK I knew that on galaxy tool dependencies page http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave the link for GATK 1.4 version but I can't figure out how to download and install it, and I noticed that GATK2 have all 1.x version features, so I installed GATK2. In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are multiple folders and files and I got really confused what I need to download. Even I choose "ZIP" to download a zip file, I counld not figure out whether it is the program package and don't know how to install it. Maybe this is the problem. But based on my understanding, GATK is just a set of java package, and all we need to do is put it into /tool-data/shared/jars folder, right? That is how I did it for GATK2. The GATK2 package include a folder called "resources" and a file called "GenomeAnalysisTK.jar" . I put them into /tool-data/shared/jars/gatk folder. I tested the installation following the instruction : http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-… And I request a key from broadinstitute and followed the instruction on http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… But the galaxy still gave me the error message as followed： ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ I guess I may made mistakes in some point: 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use it. But I really don't know how to download and install it. I can't find the correct file. 2. GATK2 works on Galaxy but I did something wrong on installing it. Could anyone help me about this? It will be greatly appreciated. Thanks. Anthonel

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Working directly with gzipped files
by Fabiano Lucchese 12 Dec '12

12 Dec '12

Hi, all. I set up a local installation of Galaxy and have been trying to reproduce inside it what I had previously accomplished with command-line scripts. One of the tools that I'm using is BWA, so I installed the "Map with BWA Illumina" tool from the tool shed. So far so good. However, when performing alignments at the command-line, I was able to directly input fastq.gz files onto BWA, which doesn`t seem to be possible inside Galaxy. Besides saving a lot of storage space, working with gzipped fastq files turned out to give me faster results too, so it's a "must have" feature for me. When I try to create a BWA task, the form complains that there isn`t any compatible file in my history. If I try to see the files contents, there's an error message complaining about their encoding. If I gunzip the files, everything works fine. Am I falling into any beginner's dumbness? Thanks in advance. F.

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Extra files saved outside of Galaxy's history?
by Gomez, Ann 12 Dec '12

12 Dec '12

Hi all, I have a pipeline involving a series of scripts, which creates directories (and many subdirectories), that I'd like to wrap for use in Galaxy. Although the contents of the folders are not the primary output of the pipeline, (and I don't want them as history items), I'd still like them to be accessible for users to double-check the contents if they so desire. However, I'm not sure where a good place to create/persist the folders would be. Although I'm running a local install on my own machine for the moment, the goal will be to move to a cluster in the near future. Does anyone have experience with this kind of thing or have any ideas? Apologies if I've missed something; I haven't found anything related on the mailing list or the wiki, except for this thread that suggests disabling the cleanup method of the JobWrapper for debugging purposes: http://dev.list.galaxyproject.org/persisting-job-working-directory-td413 8922.html. Thanks for your consideration, Ann

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some problem with the fastq interlacer
by 泽蔡 12 Dec '12

12 Dec '12

Hi all, I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer seems do not reganize the name of the pair-end reads, and treat the pair-end reads as non-pair-edn reads. Best regards

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pbs_python and torque 4.x
by Steve.Mcmahon＠csiro.au 12 Dec '12

12 Dec '12

Hi all, We are trying to get our instance of Galaxy submitting jobs to a cluster a using the staged method referred to at http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Our cluster is running Torque 4.1.3. We need to use Torque 4.x clients to be able to submit jobs to it. I've set up our Galaxy server to be able to submit jobs and stage data in and out. Galaxy can't submit jobs to the cluster, however. The problem seems to be with pbs_python. On the associated wiki there is a ticket for the problem and I have been able to reproduce it. https://oss.trac.sara.nl/pbs_python/ticket/31 Has anyone had any experience with getting pbs_python to work with Torque 4.x? Regards. Steve McMahon Solutions architect & senior systems administrator ASC Cluster Services Information Management & Technology (IM&T) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcmahon(a)csiro.au<mailto:steve.mcmahon@csiro.au> | www.csiro.au<http://www.csiro.au/> PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600

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Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
by Sachit Adhikari 12 Dec '12

12 Dec '12

Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit

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Job is waiting to run
by Fenglou Mao 11 Dec '12

11 Dec '12

I have a local galaxy server, and I built a workflow, it got stuck in one step in the middle. The computer is a 64 cores server, and no other jobs running in this server. Any idea how to trouble shooting? Thanks, Fenglou

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Installing Job Runners on a Cluster
by Ganote, Carrie L 11 Dec '12

11 Dec '12

Hi all, I could use some help getting DMRAA to run. We already have a galaxy instance with pbs running, but I'd like to connect to Torque using dmraa because we eventually intend to port over to a different resource manager. I've followed these instructions: http://apps.man.poznan.pl/trac/pbs-drmaa/wiki#Introduction http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Got dmraa installed and exported a path in my shell config: (PREFIX is long so I omitted it) DRMAA_LIBRARY_PATH=PREFIX/drmaa/lib/libdrmaa.so.1.0.12 in my universe_wsgi.ini: start_job_runners = drmaa default_cluster_job_runner = drmaa://-q tstgalxy -V/ addValue = drmaa:/// Here's my pbs_drmaa.conf: wait_thread: 0, pool_delay: 5, keep_completed: 60, user_state_dir: PREFIX/%s/jobs, I tried something simple like the add value tool. When I run it, I get the following error state: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "en_US", LANG = "C" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). The output file is actually correct, Galaxy just thinks there's an error. I get 2 files in user_state_dir with a job number and .started (empty) and .exitcode (0). Sounds like an env issue? If I run the perl script generated in the .sh file, it works fine. Output as expected. If I use local:/// it works fine with no error. I couldn't find any documentation on how to actually link dmraa to torque. Am I missing something major? Thanks in advance, Carrie Ganote

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Re-installing error persists
by Franco Caramia 11 Dec '12

11 Dec '12

Hi Greg, I have now modified the tool_dependencies.xml thank you for that.. I still have problems re-installing the tool... (need to reinstall to update the tool dependency and test it correctly) Is the reinstalling failure related to my galaxy version?? Here is the error: Server Error URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+o r+reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.reselect_tool_panel_section( trans, **kwd ) Module galaxy.web.framework:184 in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:1352 in reselect_tool_panel_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:757 in fill_template_mako >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> __M_writer(unicode(next.body())) Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> __M_writer(unicode(render_tool_dependency_section( install_tool_dependencies_check_box, [ repo_info_dict ] ))) Module _admin_tool_shed_repository_common_mako:204 in render_render_tool_dependency_section >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activa… r+reinstall&id=88ee2d7021e4dc1a#> elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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