galaxy-dev March 2014

galaxy-dev@lists.galaxyproject.org

101 participants
141 discussions

Re: [galaxy-dev] Persistent jobs in cluster queue even after canceling job in galaxy
by Ravi Alla 11 Mar '14

11 Mar '14

Hi Peter, No I am not using that option. It is currently set to false in my universe_wgsi.ini file. It says it is a new feature and not recommended, so I didn't mess with it. Thanks Ravi On Mar 11, 2014, at 11:27 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > Hi Ravi, > > Could you reply to the list? > > And actually I meant do you have "use_tasked_jobs = True" in > your universe_wsgi.ini file which is linked to the special XML > tag <parallelism> in some Galaxy Tools for splitting jobs. > Sorry, that was unclear of me. > > Peter > > > On Tue, Mar 11, 2014 at 6:24 PM, Ravi Alla <ravi.alla(a)berkeley.edu> wrote: >> Peter, >> This is a Centos linux cluster using PBS Torque job manager. By parallelization are you referring to multiple job handlers? No I am not. I barely set this server up and it is in its most basic form so far. I will add options for multiple web servers and runners once I get things working soundly. >> Thanks >> Ravi >> On Mar 11, 2014, at 11:07 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: >> >>> On Tue, Mar 11, 2014 at 5:57 PM, Ravi Alla <ravi.alla(a)berkeley.edu> wrote: >>>> Hi All, >>>> I've been able to submit jobs to the cluster through galaxy, it works great. >>>> But when the job is in queue to run (it is gray in the galaxy history pane) >>>> and I cancel the job, it still remains in queue on the cluster. Why does >>>> this happen? How can I delete the jobs in queue as well? I tried qdel >>>> <job_id> as galaxy user but it says I am not authenticated to delete the job. >>>> Any help would be greatly appreciated. >>>> Thanks >>>> Ravi. >>> >>> What kind of cluster is it? e.g. SGE? >>> >>> Are you using task splitting (parallelization)? >>> >>> Peter >>

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launching openmpi tool with Galaxy
by Olivia Doppelt-Azeroual 11 Mar '14

11 Mar '14

Dear developers, I'm trying to launch a mpi version of test tool. To do so, I have a test xml called sleep.xml but all he does is write the hostname of the machine in an output file. (command: /usr/lib64/openmpi/bin/mpirun hostname > $output) When I launch this tool as a local job (we use son of grid engine as the job scheduler), everything is ok. When i specify the following line in the universe_wsgi.xml: sleep = drmaa://-q galaxy -pe openmpi 8/ The program is launched but it is lost somewhere and juste doesn't do anything. It is just running and never ends. Does someone has an explanation for that ? Thanks in advance, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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GATK2 (from IUC) Missing reference_genome selection
by Geert Vandeweyer 10 Mar '14

10 Mar '14

Hi, I'm using the GATK2 tools from IUC, taken from the main toolshed. After configuration, I'm able to run the tools as standalone jobs, and everything works. When I add the job to a workflow, The 'Using reference genome' selection is empty (see screenshot in attachment for PrintReads tool). Just filling in the database key (hg19 in my case) allows the workflow to run correctly. When I noticed that the Unified Genotyper does not show this behaviour, I checked the XML files. After commenting out the following line (which is commented in Unified Genotyper by default) in the "Realigner Target Creator" tool, The selection drop-down menu showed correctly for RTC: <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> So I assume that this filter is conflicting with the workflow editor somehow. Is this an issue on my site only, or is this a general bug? On a side note: i'd like to be able to set the java --max_jvm_heap value on a per-gatk-tool basis without directly editing the xml files, instead of using the default heap_fraction setting. Is this possible (yet) ? Editing the XML files caused the update of toolshed_packages to fail by launching interactive diff-merge tasks when updating from the website. Kind regards, 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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NGS toolbox does not appear
by Nilaksha Neththikumara 10 Mar '14

10 Mar '14

Dear all, I installed a local instance of Galaxy to analyze some exome sequences which can not be uploaded to the online Galaxy because they are of around 3GBs. When going through galaxy tutorials , I found there is a collection of tools called NGS toolbox which is not appearing in my local instance. NGS:QC and manipulation is available but with very limited number of tools , even without fastQC. I annexed pictures of both my available instance and the galaxy I saw via tutorial video. What am I doing wrong? Thanks a lot in advance. [image: Inline image 1] Galaxy showed up on tutorial video [image: Inline image 2]Galaxy in my local instance

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Re: [galaxy-dev] Torque Exec Exception
by 分析流 09 Mar '14

09 Mar '14

hi, we can run 'qstat -x' on the command line successfully ，but nothing shows on terminal. because we have no job submitted recently. (pbs only shows jobs traced back a certain time, not the entire history) however, in case of nothing returns for 'qstat -x' command, there will be an error prompt in paster.log file, which we think it is not properly logged (although the command is actually successfully finished). We will look into code to make sure for that if we have time. Just for your reference. ------------------ Original ------------------ From: "Nate Coraor"<nate(a)bx.psu.edu>; Date: Fri, Mar 7, 2014 10:34 PM To: "ngsflow(a)hygenomics.com"<ngsflow(a)hygenomics.com>; Cc: "galaxy-dev"<galaxy-dev(a)lists.bx.psu.edu>; "吴一雷"<wuyl(a)hygenomics.com>; Subject: Re: [galaxy-dev] Torque Exec Exception Hello, Are you able to run `qstat -x` on the command line on the remote system? What's the output? --nate On Thu, Mar 6, 2014 at 1:01 PM, ngsflow(a)hygenomics.com <ngsflow(a)hygenomics.com> wrote: > hi all: > > > > galaxy.jobs.runners.cli_job.torque WARNING 2014-03-07 11:23:33,764 No valid > qstat XML return from `qstat -x`, got the following: > > galaxy.jobs.runners ERROR 2014-03-07 11:23:33,765 Unhandled exception > checking active jobs > > Traceback (most recent call last): > > File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/__init__.py", line > 339, in monitor > > self.check_watched_items() > > File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 150, > in check_watched_items > > job_states = self.__get_job_states() > > File "/share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py", line 202, > in __get_job_states > > job_states.update(job_interface.parse_status(cmd_out.stdout, job_ids)) > > TypeError: 'NoneType' object is not iterable > > > #qmgr -c "p q batch" > > create queue batch > set queue batch queue_type = Execution > set queue batch enabled = True > set queue batch started = True > > Finish the torque tasks ， throw exceptions in the log file。 > ________________________________ > ngsflow(a)hygenomics.com > > ___________________________________________________________ > 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/

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how to manage multiple tool versions
by ruiwang.sz 08 Mar '14

08 Mar '14

Hi Guys, I'm sorry to post multiple times for the same question. Now I removed all the specifics of my problem and I only want someone to point me to the right documentation. Admins, I know you are busy, but don't you want more people to benefit from this platform? When galaxy upgraded it started using the tool_shed version of the tool and killed the tools we installed ourselves. Right now we have both versions. How should we manage this situation properly if we don't want the tool_shed version and want to keep using what we had before? Nate said that MACS came with galaxy before. I didn't know that. From the day we started using MACS it was installed by ourselves. Not sure if that caused the problem. Thanks, Rui

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Re: [galaxy-dev] tool trouble
by Briand, Sheldon 07 Mar '14

07 Mar '14

Hi, I've finally figured out what is happening with galaxy on my end regarding tools not showing up in the menu. I moved my install to a new larger file system and started from scratch wiping out the database to rule out my having messed up the galaxy instance. The first tool I tried was one I had "successfully" installed on my previous setup. I tried to install package_cufflinks_2_1_1. One thing I noticed during the initial install setup screens is that it didn't ask me where I wanted to put the cufflinks tool in my menu. After the package had successfully installed the tool does not show up in the Analyze data tool list. I then tried to install the cufflinks tool which has the repository dependency of package_cufflinks_2_1_1. During the initial install screens I'm given the option of putting the tool in one of my existing tool panel sections or adding a new one. I installed and the tool shows up in the Analyze Data tool list where it's expected. I'm just wondering if this is expected behavior or it's something I've configured wrong. In cases such as bowtie 1 (I could use bowtie 0_12_7 and use the bowtie wrapper), I only have the package option and so I can't get the tool to appear in my menu. Thanks! -Sheldon -----Original Message----- From: Briand, Sheldon Sent: Monday, March 03, 2014 2:16 PM To: 'Greg Von Kuster' Subject: RE: [galaxy-dev] tool trouble Hi, Not sure if you were still scratching your head about this one. I am going to be moving my galaxy install to a new larger file system and put it in production so I thought I would do a new install as my current one was just testing. If you were still going to be looking at it don't bother. Thanks for all you had done on it up to now. Cheers! -Sheldon -----Original Message----- From: Briand, Sheldon Sent: Friday, February 28, 2014 6:38 PM To: 'Greg Von Kuster' Cc: galaxy-dev(a)lists.bx.psu.edu Subject: RE: [galaxy-dev] tool trouble Hi Greg, Also for bowtie2. I can confirm that it doesn't have an entry in the shed_tool_conf.xml file. Sorry I didn't mention these before. Its been a long week and there obviously was a problem between my chair and keyboard. :) -Sheldon ________________________________________ From: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of Briand, Sheldon [Sheldon.Briand(a)ssc-spc.gc.ca] Sent: Friday, February 28, 2014 6:02 PM To: 'Greg Von Kuster' Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] tool trouble Hi, So those are the ones that work. One of the ones that doesn't work is bowtie2: tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 16:03:14,476 Adding an entry for revision 017a00c265f1 of repository package_bowtie2_2_1_0 owned by devteam to repository_dependencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 16:03:14,490 Adding an entry for revision 017a00c265f1 of reposito ry package_bowtie2_2_1_0 owned by devteam to installed_repository_dependencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 16:03:14,502 Adding an entry for revision 017a00c265f1 of reposito ry package_bowtie2_2_1_0 owned by devteam to tool_dependencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 16:03:14,516 Adding an entry for revision 017a00c265f1 of reposito ry package_bowtie2_2_1_0 owned by devteam to installed_tool_dependencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 16:03:45,046 Adding an entry for version 2.1.0 of package bowtie2 to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. galaxy.tools.data DEBUG 2014-02-28 16:04:39,615 Loaded tool data table 'bowtie2_indexes' No tool ID loaded (loaded from the .xml file in the shed_tools dir?). And no file .xml fileor .py file in the shed_tools directory. But a successful install in the admin interface. I appreciate you looking into this for me. -Sheldon From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Friday, February 28, 2014 5:51 PM To: Briand, Sheldon Subject: Re: [galaxy-dev] tool trouble Hi Sheldon, I'm not sure what to advise you to do here as all of the information looks ok. It's not clear at all why the tools are not displayed in your tool panel. Are they loaded but simply hidden (set to not be visible)? Did you make any changes to your integrated_tool_panel.xml file? If not, try deleting it an restartign your Galaxy server (the file gets automatically recreated if missing). I can't think of anything else to take a look at on this. Sorry I'm not able to be very helpful here. On Feb 28, 2014, at 4:24 PM, "Briand, Sheldon" <Sheldon.Briand(a)SSC-SPC.gc.ca<mailto:Sheldon.Briand@SSC-SPC.gc.ca>> wrote: Hi, Yes for deseq and sam2count: <section id="ngs:rnaseq" name="NGS:RNAseq" version=""> <tool file="toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e…<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…>" guid="too lshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0>"> <tool_shed>toolshed.g2.bx.psu.edu<http://bx.psu.edu></tool_shed> <repository_name>deseq_and_sam2counts</repository_name> <repository_owner>nikhil-joshi</repository_owner> <installed_changeset_revision>a49aff09553e</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0></id> <version>1.0.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e…<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…>" gu id="toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1…<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0.0>"> <tool_shed>toolshed.g2.bx.psu.edu<http://bx.psu.edu></tool_shed> <repository_name>deseq_and_sam2counts</repository_name> <repository_owner>nikhil-joshi</repository_owner> <installed_changeset_revision>a49aff09553e</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1…<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0.0></id> <version>1.0.0</version> </tool> </section> galaxy.tools DEBUG 2014-02-28 16:10:18,298 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/deseq/1.0.0>, ve rsion: 1.0.0 into tool panel. galaxy.tools DEBUG 2014-02-28 16:10:18,310 Loaded tool id: toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1…<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/sam2counts/1.0>. 0, version: 1.0.0 into tool panel. -Sheldon From: Greg Von Kuster [mailto:greg@bx.psu.edu<http://bx.psu.edu>] Sent: Friday, February 28, 2014 5:19 PM To: Briand, Sheldon Cc: galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] tool trouble I assume you have a proper entry for the deseq_and_sam2count repository in your shed_tool_conf.xml file (please confirm). What does the relevant section of your Galaxy paster log show when attempts are made to load the tools contained in this repository at server startup? On Feb 28, 2014, at 4:02 PM, "Briand, Sheldon" <Sheldon.Briand(a)SSC-SPC.gc.ca<mailto:Sheldon.Briand@SSC-SPC.gc.ca>> wrote: Hi, Yep that's what I have. Here is deseq: find . -name "*deseq*" ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq._r.sample.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq.xml.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq/deseq.xml.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq/deseq._r.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/.hg/store/data/deseq/deseq._r.i<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.R<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/deseq_and_sam2counts/deseq/deseq.xml<http://bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts/a49aff09553e/dese…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/package_deseq2_1_0_17<http://bx.psu.edu/repos/iuc/package_deseq2_1_0_17> ./shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/package_deseq2_1_0_17/0e80b1827773/package_deseq2_1_0_17<http://bx.psu.edu/repos/iuc/package_deseq2_1_0_17/0e80b1827773/package_dese…> ./galaxy-dist/dependancies/R_3_0_1/3.0.1/iuc/package_deseq2_1_0_17 ./galaxy-dist/dependancies/deseq2 ./galaxy-dist/dependancies/deseq2/1.0.17/iuc/package_deseq2_1_0_17 ./galaxy-dist/dependancies/deseq2/1.0.17/iuc/package_deseq2_1_0_17/0e80b1827773/deseq2 -Sheldon From: Greg Von Kuster [mailto:greg@bx.psu.edu<http://bx.psu.edu>] Sent: Friday, February 28, 2014 4:59 PM To: Briand, Sheldon Cc: galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] tool trouble Hello Sheldon, What is the configuration setting you are using for the location to install repositories? This is defined by the tool_path attribute of the <toolbox> tag in your shed_tools_conf.xml file. The default is: <toolbox tool_path="../shed_tools"> On Feb 28, 2014, at 3:47 PM, "Briand, Sheldon" <Sheldon.Briand(a)SSC-SPC.gc.ca<mailto:Sheldon.Briand@SSC-SPC.gc.ca>> wrote: Hi, No joy on the migration strategy. Deseq is example of a tool that I installed successfully yesterday. Do you mean that you installed the deseq repository from the main tool shed: http://toolshed.g2.bx.psu.edu/view/nikhil-joshi/deseq_and_sam2counts and that its contained deseq tool "DE Seq (version 1.0.0)" was properly displayed in your Galaxy tool panel? If so, what is now happening? Bowtie2 is an example of a tool that isn't showing up even though the web interface indicates that it is successfully installed. Can you uninstall the repsository and reinstall it? If so, what happens? Here is my directory structure relating to bowtie2: $ find . -name "*bowtie2*" ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2<http://bx.psu.edu/repos/devteam/bowtie2> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0<http://bx.psu.edu/repos/devteam/package_bowtie2_2_1_0> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/package_bowtie2_2_1_0/017a00c265f1/package_bowtie2_2_1_0<http://bx.psu.edu/repos/devteam/package_bowtie2_2_1_0/017a00c265f1/package_…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/.hg/store/data/tool-data/bowtie2__indices.loc.sample.i<http://bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/.hg/store/data…> ./shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/tool-data/bowtie2_indices.loc.sample<http://bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tophat2/tool-data/bowt…> ./galaxy-dist/.hg/store/data/tool-data/bowtie2__indices.loc.sample.i ./galaxy-dist/.hg/store/data/tools/sr__mapping/bowtie2__wrapper.xml.i ./galaxy-dist/.hg/store/data/tools/sr__mapping/bowtie2__wrapper.py.i ./galaxy-dist/.hg/store/data/test-data/bowtie2 ./galaxy-dist/tool-data/bowtie2_indices.loc.sample ./galaxy-dist/tool-data/bowtie2_indices.loc ./galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/bowtie2_indices.loc<http://bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/bowtie2_indices.loc> ./galaxy-dist/dependancies/samtools/0.1.18/devteam/bowtie2 ./galaxy-dist/dependancies/samtools/0.1.19/iuc/package_samtools_0_1_19/00e17a794a2e/bin/bowtie2sam.pl ./galaxy-dist/dependancies/bowtie2 ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/bowtie2 ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0 ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-align ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build-debug ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-inspect-debug ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2 ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-inspect ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-align-debug ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build [galaxy@eugene galaxy]$ cd shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/<http://bx.psu.edu/repos/devteam/bowtie2/> I seem to be missing the .py and .xml files in the shed_tools directory. -Sheldon From: Briand, Sheldon Sent: Friday, February 28, 2014 2:11 PM To: 'Greg Von Kuster' Subject: RE: [galaxy-dev] tool trouble Hi, Thanks for getting back to me. I didn't get your first reply (email trouble here) when I sent my second email. I have not played with the sql tables. I think my problem is that I need to run tool migration scripts. The reinstall log I sent was for tophat 2. It didn't show up in shed_tool_conf.xml after the update so I thought it had once again failed. After I sent the email I noticed that tophat2 had shown up in the tool menu (not where I wanted it but it was there). So I looked around and there was an entry in migrated_tools_conf.xml. I think the tools I am missing are because I likely missed the migration step. I'll try that first and report back. Cheers, -Sheldon From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: Friday, February 28, 2014 11:04 AM To: Briand, Sheldon Cc: galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] tool trouble Hello Briand, This may take some back-and-forth with you to understand the steps you have taken so far. Successfully installing a repository that contains tools usually results in the tools being displayed in the Galaxy tool panel. However, there may be issues that result in the tools not properly loading. This often occurs when you stop and restart your Galaxy instance. Your Galaxy pasxter log will include information about any tool that does not properly load. Uninstalling and reinstalling the repository will usually not have any affect on this. On Feb 28, 2014, at 9:17 AM, "Briand, Sheldon" <Sheldon.Briand(a)ssc-spc.gc.ca<mailto:Sheldon.Briand@ssc-spc.gc.ca>> wrote: Hi, I've been poking around a bit more. It looks as though galaxy isn't actually downloading and installing the tools. The tool status changes to installed in the web interface and postgres but the tool is not present on disk. What is present on disk? If you install a repository with tools, the repository revision's contents should be on disk. However, if the repository is uninstalled, disk files are deleted. Do you have repositories that are installed but do not have any files on disk? The log below shows no download and make of the tool and dependancies. Hopefully the log gives a bit more information. Sorry for the second email. tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:48,567 Updating an existing row for repository 'tophat2' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:48,714 Creating repository dependency objects... The log looks ok at first inspection, but it's not useful without more information. From: galaxy-dev-bounces(a)lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu<mailto:dev-bounces@lists.bx.psu.edu>] On Behalf Of Briand, Sheldon Sent: Thursday, February 27, 2014 8:18 PM To: galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] tool trouble Hi, I'm having trouble with some of my tools not appearing in the Analyze Data menu. I've successfully installed the tools via the manage installed tool shed repositories(so they are installed to disk). I have tried uninstalling and installing again. The above should not be necessary. When you install, are you checking the optional checkboxes to install repository dependencies and tool dependencies? If so, are they installing as well? The tool installs but does not appear in the menu. Do you have an example of a repository that contains tools that installls corruptly, but the tools do not load into the tool panel? Other tools install the menu updates just fine. Do you have an example of a repsoitory that contains tools that do show up in the tool panel after successfule repository installation? This is probably due to me corrupting the misbehaving tools installation somehow. I'm guessing that I need to uninstall the tool and wipe some postgres entries. I strongly advise not manually changing inaything in your database suing sql commands. If you have done this, it could be the cause of the behavor you are describing. The Galaxy UI or API should be used. Greg Von Kuster My shed tool path: <toolbox tool_path="../shed_tools"> My current version: parent: 12441:dc067a95261d Added tag release_2014.02.10 for changeset 5e605ed6069f branch: stable Could someone point me in the right direction? 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<mailto:sheldon.briand@ssc-spc.gc.ca> ___________________________________________________________ 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/

2 1

pbs runner deserializes server names as unicode
by Eric Badger 07 Mar '14

07 Mar '14

Hi there, I've run into an issue with the pbs runner involving pbs server name strings becoming 'unicode' rather than 'str'. The pbs_python lib can't pass unicode strings down to the C library, which results in this failure: https://gist.github.com/anonymous/9352218 The very top line of log output in the above gist is due to a line I added to runners/pbs.py: https://gist.github.com/anonymous/9352101#file-pbs-py-L16 I can reproduce this as follows: 1. Start a job using pbs runner. 2. While the job is still running, restart galaxy. 3. Error now appears in the logs. It seems that this is happening because, when deserializing job.destination_params from the database, the strings are converted to unicode. The jobs in this state are effectively stuck, since galaxy can't connect to check on their status. I'm not sure where the best place to address this would be; thoughts? This is on an up to date galaxy-dist with Torque 2.5.13. Thanks, Eric

2 4

Shared Data as options for tools
by Dooley, Shane 07 Mar '14

07 Mar '14

Hi all, I have looked and I found only one place<http://www.mail-archive.com/galaxy-dev%40lists.bx.psu.edu/msg04237.html> where this question was asked back in 2012 but no answers. My question is how can I specify a dataset in a shared library without importing the dataset to my current history? Ideally it would be something like param< type="history_dataset" ...> but if that isn't an option is there a way to plugin ajax or some other scripting to grab options to fill the list? Shane This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. The dupont.com<http://dupont.com/> web address will continue in use for a transitional period for communications sent or received on behalf of DuPont Performance Coatings., which is not affiliated in any way with the DuPont Company. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html

1 0

LWR questions
by Jun Fan 07 Mar '14

07 Mar '14

Hi all, LWR sounds very attractive and promising. However how to program on galaxy side to utilize LWR server is not thoroughly documented. I have several questions to ask: 1. I separate the tool wrappers (.xml) and the applications (.pl, .py etc) in two different folders. In the traditional way it works fine. When I use the legacy way of using LWR (adding galaxy:tool_runners section in the universal_wsgi.ini file), the error message says that the application cannot be found. Does the executable have to be in the same folder with the wrapper? 2. In the thread http://dev.list.galaxyproject.org/Managing-Data-Locality-td4662438.html#a46… John only mentioned $GALAXY_ROOT/databases/files, does this mean that the dynamic multiple output is not supported as it uses $GALAXY_ROOT/databases/tmp folder? 3. What types of files are supposed to be stored under tools directory (tool_files), working directory (working), inputs (inputs), configs directory (configs), all of which are subfolders of ${staging_directory}/${job_identifier}? 4. Is there file size limit on the LWR server? Best regards! Jun

2 3

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galaxy-dev March 2014