- galaxy-dev - lists.galaxyproject.org

Creating cluster_files_directory (default database/pbs)
by Peter Cock 25 Jan '16

25 Jan '16

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). As part of this, we've tried setting up a fresh > installation on a new VM which has thrown up some issues. > > [snip] We eventually got Galaxy to talk to SGE and submit jobs successfully as the individual user's Linux account, with external_chown_script.py being called to handle ownership of the files. One small stumbling block was missing the cluster_files_directory directory. https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample says: # If using a cluster, Galaxy will write job scripts and stdout/stderr to this # directory. #cluster_files_directory = database/pbs According the the current code, this is still the default value being used: https://github.com/galaxyproject/galaxy/blob/274af50792aaaf367520c22d7c13e2… However, Galaxy itself did not seem to create the cluster_files_directory directory - and there doesn't seem to be a ready-made pbs folder in the git repository. Should that happen automatically? At one stage, run.sh would create database/files and database/tmp - I'm note sure what that happens now: https://github.com/galaxyproject/galaxy/commit/4d720d63c631862778e54bd68c4e… https://github.com/galaxyproject/galaxy/commit/7560751dc87492471880c82b0085… Peter

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Re: [galaxy-dev] errors installing tool dependencies...
by Nicola Soranzo 25 Jan '16

25 Jan '16

Hi Edgar, indeed your bug was fixed long ago, please see http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-t… You should really move to the GitHub repository and update to the latest 15.07 or (better) to 15.10 . Cheers, Nicola On 25/01/16 17:09, Fernandez Edgar wrote: > > [galaxy@galaxy_sever galaxy-prod]$ hg id -i > > f6683935f81a+ > > *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la > Communication*//* > > */Université de Montréal/* > > *//* > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568//* > > *From:*Nicola Soranzo [mailto:nicola.soranzo@gmail.com] *On Behalf Of > *Nicola Soranzo > *Sent:* January-25-16 12:05 PM > *To:* Fernandez Edgar <edgar.fernandez(a)umontreal.ca>; Martin Čech > <marten(a)bx.psu.edu>; galaxy-dev(a)bx.psu.edu > *Subject:* Re: [galaxy-dev] errors installing tool dependencies... > > Hi Edgar, > this smells like an old fixed bug, what version of Galaxy are you running? > > Cheers, > Nicola > > On 25/01/16 14:22, Fernandez Edgar wrote: > > Hello Martin, > > Thank you! > > Your instructions for my problem with Perl package worked. > > For the URL of hmmer, it is wrong and I will report it like you > suggested it. > > Finally, a new error occurred for bowtie. > > Would you please take a look? > > My Sincere Salutations, > > *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la > Communication > > */Université de Montréal/* > > *//* > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568* > > *From:*Martin Čech [mailto:marten@bx.psu.edu] > *Sent:* January-22-16 2:34 PM > *To:* Fernandez Edgar <edgar.fernandez(a)umontreal.ca> > <mailto:edgar.fernandez@umontreal.ca>; galaxy-dev(a)bx.psu.edu > <mailto:galaxy-dev@bx.psu.edu> > *Subject:* Re: [galaxy-dev] errors installing tool dependencies... > > Hi Edgar, > * > *for the package_perl issue please try installing updates to the > dependencies (package_gnu_coreutils and package_perl in their > respective versions) and then return to this screen and click the > 'repository action' button and then 'manage dependencies' from the > menu. Uninstall both dependencies (gnu_coreutil and perl) and then > install them again. > > That should pick up the newest versions and you should be set. > > Regarding the hmmer that is a more prosaic problem, at the time of > the installation the software was not available at the given URL. > Check the machine's internet connection and if it is ok try > downloading the file manually. If it succeeds the problem might > have been on their side and is ok now. If it does not the problem > can still be on their side and in that case either wait a bit and > try again or report the issue > athttps://github.com/galaxyproject/tools-iuc/issues > > thank you for using Galaxy. > > Martin > > On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar > <edgar.fernandez(a)umontreal.ca > <mailto:edgar.fernandez@umontreal.ca>> wrote: > > Hello guys, > > Happy new year everyone! > > Wish you all the best! > > I have a couple of small problems I’ve attached as pictures… > > Can you please help me? > > INFO: My galaxy installation and database is updated today! > > My sincere salutations, > > *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la > Communication > > */Université de Montréal/* > > *//* > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568 * > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >

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Re: [galaxy-dev] errors installing tool dependencies...
by Fernandez Edgar 25 Jan '16

25 Jan '16

Hello guys, Happy new year everyone! Wish you all the best! I have a couple of small problems I’ve attached as pictures… Can you please help me? INFO: My galaxy installation and database is updated today! My sincere salutations, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568

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Question about FastqMcf installed from the Galaxy toolshed
by Audrey Michel 25 Jan '16

25 Jan '16

Hi Galaxy team, One of our users requested for FastqMcf <http://143.239.109.139:9093/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Fre…> to be installed on our Galaxy server as they want to use it to remove duplicate reads in their FASTQ file. However, the FastqMcf <http://143.239.109.139:9093/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Fre…> tool version that we installed from the Galaxy toolshed, does not have the parameter for removing duplicates - see screenshot attached (on the command line version -D N Remove duplicate reads) . Could you advise if the "remove duplicate reads" parameter could be included in the galaxy version of the tool or should we explain to our user that the Galaxy implementation of this tool cannot be used from removing duplicates? Thanks in advance for your reply, Audrey

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Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS
by Oksana Korol 25 Jan '16

25 Jan '16

Thanks, Bjoern! For my local install of Galaxy, logging in as a user worked and the icon is showing up (although I still had to manually go and change permissions on all the mako templates in ./database/compiled_templates directory). But our production instance of Galaxy (also v15.07 on CentOS 6.7) does not show the chart-symbol for Phyloviz, even when I'm logged in as a user. In production, it is not a clean install, but an upgrade from previous versions, so it is harder to figure out what's going on. There are no errors in the logs, so I'm still looking for any kind of clues of what could have gone wrong with the visualization. Cheers, Oksana Message: 1 > Date: Sat, 23 Jan 2016 19:55:47 +0100 > From: Björn Grüning <bjoern.gruening(a)gmail.com> > To: Oksana Korol <okorol(a)gmail.com>, > galaxy-dev(a)lists.galaxyproject.org > Subject: Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS > Message-ID: <56A3CCB3.9020503(a)gmail.com> > Content-Type: text/plain; charset=utf-8 > > Hi Oksana, > > this work for me in 16.01 (upcoming). Please make sure you are logged > into your Galaxy as some user, not anonymous and than the Phyloviz > Visualisation will be available from the small chart-symbol next to the > (i) symbol. > > Hope this helps, > Bjoern > > Am 22.01.2016 um 23:53 schrieb Oksana Korol: > > Hi, > > > > I'm having trouble getting visualization icons, like Phyloviz, to show > > up on my Galaxy instance running in CentOS 6.7. Here are the steps I > > took, expecting it to work: > > > > 1. cloned Galaxy tag v15.07 (that's the version we need to run in > > production) > > > > 2. Followed the steps in > https://wiki.galaxyproject.org/VisualizationSetup > > - Renamed datatypes_conf.xml.sample to > > datatypes_conf.xml > > - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit > > - Installed BED Tools > > - Added above tools to my user path (galaxy_utils dir is where > > wigToBigWig and others are): > > > /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/*home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin > > * > > 3. Started Galaxy. > > > > 4. Uploaded a newick tree file (nhx), which is known to be displayable > > in phyloviz on a Ubuntu instance of Galaxy > > > > 5. Made sure the datatype is nhx > > > > 6. Expecting to see a Phyloviz "graph" icon on the left, when I expand > > the file in history, but there is nothing there. > > > > At this point I don't know where to dig to find how I can fix it. Any > > feedback, including your own stories for visualization setup or how I > > can debug what's not being picked up where, would be greatly appreciated. > > > > Cheers, > > Oksana > > -- > > :: > > Oksana Korol > > dataquarry.blogspot.ca <http://dataquarry.blogspot.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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > >

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configuration management, tool shed and tool revisions
by Steve.Mcmahon＠csiro.au 25 Jan '16

25 Jan '16

Hi, We are using Puppet to manage the configuration for VMs for our development and production Galaxy instances. We would like to be able to specify tool shed tools and their revisions and have Puppet ensure that they are installed. Our Puppet code makes use of the "install_tool_shed_repositories.py" script and a script based on that which checks to see whether a particular tool and revision is installed. We are finding that if we don't specify the latest revision of a tool that the "install_tool_shed_repositories.py" script fails. Is this what others experience? I know other sites are doing configuration management with Ansible. What approach are these sites taking for ensuring tools are installed or are these sites doing the tool installations outside of configuration management? Regards. Steve McMahon Solution Architect and Senior System Administrator | Scientific Computing Information Management and Technology CSIRO T +61 2 6214 2968 Alt +61 4 0077 9318 steve.mcmahon(a)csiro.au<mailto:steve.mcmahon@csiro.au> | www.csiro.au 1 Wilf Crane Crescent, Yarralumla ACT 2600 PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.

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Setting up visualization on Galaxy on CentOS
by Oksana Korol 23 Jan '16

23 Jan '16

Hi, I'm having trouble getting visualization icons, like Phyloviz, to show up on my Galaxy instance running in CentOS 6.7. Here are the steps I took, expecting it to work: 1. cloned Galaxy tag v15.07 (that's the version we need to run in production) 2. Followed the steps in https://wiki.galaxyproject.org/VisualizationSetup - Renamed datatypes_conf.xml.sample to datatypes_conf.xml - Downloaded wigToBigWig, bedGraphToBigWig, and faToTwoBit - Installed BED Tools - Added above tools to my user path (galaxy_utils dir is where wigToBigWig and others are): /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/galaxyuser/bin:/home/galaxyuser/bin:/home/galaxyuser/galaxy_utils:/home/galaxyuser/bin:/ *home/galaxyuser/galaxy_utils:/home/galaxyuser/galaxy_utils/BEDTools/bedtools2/bin* 3. Started Galaxy. 4. Uploaded a newick tree file (nhx), which is known to be displayable in phyloviz on a Ubuntu instance of Galaxy 5. Made sure the datatype is nhx 6. Expecting to see a Phyloviz "graph" icon on the left, when I expand the file in history, but there is nothing there. At this point I don't know where to dig to find how I can fix it. Any feedback, including your own stories for visualization setup or how I can debug what's not being picked up where, would be greatly appreciated. Cheers, Oksana -- :: Oksana Korol dataquarry.blogspot.ca

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Adding a5_pipeline.pl to galaxy
by Raphenya, Amogelang 22 Jan '16

22 Jan '16

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Rocks cluster; jobs run but Galaxy can't find jobid when submitted via drmaa
by Eric Shell 20 Jan '16

20 Jan '16

I am trying to get a Galaxy instance running on a Rocks cluster. I am able to run jobs with the local runner at this point, but I am having an issue with the drmaa runner that I haven't been able to fix. When I submit a job in Galaxy it is successfully submitted to the cluster and runs to completion according to qacct, but Galaxy just reports "failure running job". Here's what is written to paster.log when I submit a job: 69.181.235.240 - - [19/Jan/2016:11:24:31 -0700] "GET > /api/histories/fb86c918c0d3d33b/contents?dataset_details=bae154fe2294752e%2C6fe732485990d2ac%2C604c4e6e60e997bc%2Cf015f1cb819ec50e%2C9f6f4b3cb6cf43eb%2C3d13d598882b6eb8%2C551006fddcb290ae%2C10b9bbc646c48387%2C7670dfdf35146bc5%2Ce0ec2cf59f1fc79e%2Cee30922e5e4854db%2C9e7a0ba216194210 > HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT > 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/47.0.2526.111 Safari/537.36" > 69.181.235.240 - - [19/Jan/2016:11:24:38 -0700] "GET > /tool_runner/data_source_redirect?tool_id=ucsc_table_direct1 HTTP/1.1" 302 > - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; > x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 > Safari/537.36" > galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:42,801 Handled output > (327.778 ms) > galaxy.tools.actions.__init__ INFO 2016-01-19 11:24:43,236 Verified access > to datasets (0.023 ms) > galaxy.tools.execute DEBUG 2016-01-19 11:24:43,343 Tool > [ucsc_table_direct1] created job [7019] (919.481 ms) > 69.181.235.240 - - [19/Jan/2016:11:24:42 -0700] "POST /tool_runner > HTTP/1.1" 200 - "https://genome.ucsc.edu/cgi-bin/hgTables" "Mozilla/5.0 > (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/47.0.2526.111 Safari/537.36" > galaxy.jobs DEBUG 2016-01-19 11:24:44,056 (7019) Working directory for > job is: /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 > galaxy.jobs.handler DEBUG 2016-01-19 11:24:44,070 (7019) Dispatching to > sge runner > galaxy.jobs DEBUG 2016-01-19 11:24:44,378 (7019) Persisting job > destination (destination id: sge_default) > galaxy.jobs.runners DEBUG 2016-01-19 11:24:44,403 Job [7019] queued > (332.423 ms) > galaxy.jobs.handler INFO 2016-01-19 11:24:44,444 (7019) Job dispatched > 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET /api/genomes > HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT > 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/47.0.2526.111 Safari/537.36" > 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET > /api/datatypes?extension_only=False& HTTP/1.1" 200 - " > https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" > 69.181.235.240 - - [19/Jan/2016:11:24:44 -0700] "GET > /history/current_history_json HTTP/1.1" 200 - " > https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" > galaxy.jobs.runners DEBUG 2016-01-19 11:24:46,399 (7019) command is: > python /campusdata/galaxy/galaxy/tools/data_source/data_source.py > /campusdata/galaxy/galaxy/database/files/011/dataset_11361.dat 0; > return_code=$?; python > "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/set_metadata_IaPURP.py" > "/campusdata/galaxy/galaxy/database/tmp/tmp9Qt0cv" > "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/galaxy.json" > "/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_in_HistoryDatasetAssociation_13512_oucw5s,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_kwds_HistoryDatasetAssociation_13512_ZrUbrF,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_out_HistoryDatasetAssociation_13512_twCvq7,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_results_HistoryDatasetAssociation_13512_FO1cy9,/campusdata/galaxy/galaxy/database/files/011/dataset_11361.dat,/campusdata/galaxy/galaxy/database/job_working_directory/007/7019/metadata_override_HistoryDatasetAssociation_13512_Z_cUTF" > 5242880; sh -c "exit $return_code" > galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:46,787 (7019) submitting > file > /campusdata/galaxy/galaxy/database/job_working_directory/007/7019/galaxy_7019.sh > galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:46,808 (7019) native > specification is: -R y -pe mpi 8 -q small.q > galaxy.jobs DEBUG 2016-01-19 11:24:46,828 (7019) Changing ownership of > working directory with: /usr/bin/sudo -E scripts/external_chown_script.py > /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 eshell > 100000 > galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:47,020 (7019) submitting > with credentials: eshell [uid: 38559] > galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:47,129 (7019) Job script > for external submission is: > /campusdata/galaxy/galaxy/database/pbs/7019.jt_json > galaxy.jobs.runners.drmaa INFO 2016-01-19 11:24:47,130 Running command > ['/usr/bin/sudo', '-E', 'scripts/drmaa_external_runner.py', '38559', > '/campusdata/galaxy/galaxy/database/pbs/7019.jt_json'] > galaxy.jobs.runners.drmaa INFO 2016-01-19 11:24:47,981 (7019) queued as > 116563 > galaxy.jobs DEBUG 2016-01-19 11:24:48,198 (7019) Persisting job > destination (destination id: sge_default) > galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:48,823 (7019/116563) > state change: job is queued and active > 69.181.235.240 - - [19/Jan/2016:11:24:45 -0700] "GET > /api/histories/fb86c918c0d3d33b/contents?dataset_details=bae154fe2294752e%2C6fe732485990d2ac%2C604c4e6e60e997bc%2Cf015f1cb819ec50e%2C9f6f4b3cb6cf43eb%2C3d13d598882b6eb8%2C551006fddcb290ae%2C10b9bbc646c48387%2C7670dfdf35146bc5%2Ce0ec2cf59f1fc79e%2Cee30922e5e4854db%2C9e7a0ba216194210 > HTTP/1.1" 200 - "https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT > 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/47.0.2526.111 Safari/537.36" > galaxy.jobs.runners.drmaa DEBUG 2016-01-19 11:24:53,532 (7019/116563) > state change: job is running > galaxy.jobs WARNING 2016-01-19 11:24:53,922 (7019) Ignoring state change > from 'error' to 'running' for job that is already terminal > 69.181.235.240 - - [19/Jan/2016:11:24:54 -0700] "GET > /api/histories/fb86c918c0d3d33b/contents HTTP/1.1" 200 - " > https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" > 69.181.235.240 - - [19/Jan/2016:11:24:55 -0700] "GET > /api/histories/fb86c918c0d3d33b HTTP/1.1" 200 - " > https://galaxy.soe.ucsc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.111 Safari/537.36" > galaxy.jobs.runners.drmaa INFO 2016-01-19 11:25:06,240 (7019/116563) job > left DRM queue with following message: code 18: The job specified by the > 'jobid' does not exist. > galaxy.jobs DEBUG 2016-01-19 11:25:06,412 (7019) Changing ownership of > working directory with: /usr/bin/sudo -E scripts/external_chown_script.py > /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 galaxy > 59997 > galaxy.jobs DEBUG 2016-01-19 11:25:06,622 (7019) Changing ownership of > working directory with: /usr/bin/sudo -E scripts/external_chown_script.py > /campusdata/galaxy/galaxy/database/job_working_directory/007/7019 galaxy > 59997 'qacct -j -o eshell' shows that job 7019 completed, though: qname all.q > hostname campusrocks2-0-4.local > group users > owner eshell > project NONE > department defaultdepartment > jobname g7019_ucsc_table_direct1_eshell_ucsc_edu > jobnumber 116563 > taskid undefined > account sge > priority 0 > qsub_time Tue Jan 19 11:24:47 2016 > start_time Tue Jan 19 11:24:53 2016 > end_time Tue Jan 19 11:25:05 2016 > granted_pe mpi > slots 8 > failed 0 > exit_status 0 > ru_wallclock 12 > ru_utime 9.285 > ru_stime 0.908 > ru_maxrss 98384 > ru_ixrss 0 > ru_ismrss 0 > ru_idrss 0 > ru_isrss 0 > ru_minflt 81778 > ru_majflt 2 > ru_nswap 0 > ru_inblock 6728 > ru_oublock 184 > ru_msgsnd 0 > ru_msgrcv 0 > ru_nsignals 0 > ru_nvcsw 13952 > ru_nivcsw 301 > cpu 10.192 > mem 2.326 > io 0.150 > iow 0.000 > maxvmem 448.820M > arid undefined Why does Galaxy not see the job after it has been submitted to the cluster? Thanks in advance for your help! -- Eric Shell UNIX Software & Google Apps Administrator Baskin School of Engineering UC Santa Cruz 831 459 4919

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Data Collection collection_type list:list
by Anmol Hemrom 20 Jan '16

20 Jan '16

Hi, I was wondering if creating data collection of collection_type="list:list" is possible? Because I can see only list, pair and list of pairs options available. Why I am asking this question is because I saw this snippet from cuffdiff tool which includes collection_type="list:list" as below. <when value="CONDITION_REPLICATE_LIST"> <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> </when> Thanks Anmol

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