Hello Dave, Here is the full log info for the failed fastx runs
galaxy.jobs.runners.local DEBUG 2013-10-14 14:24:32,512 (306) executing: cat '/Volumes/Jose-Drobo/WholeGenomeSequencingDataOfInterest/Ruvkun_mut16_smallRNAs/SRR087428/SRR087428.fastq' | fastx_reverse_complement -Q 64 -v -o '/Volumes/Jose-Drobo/galaxy-dist/database/files/000/dataset_313.dat' galaxy.jobs DEBUG 2013-10-14 14:24:32,581 (306) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-10-14 14:24:32,722 execution finished: cat '/Volumes/Jose-Drobo/WholeGenomeSequencingDataOfInterest/Ruvkun_mut16_smallRNAs/SRR087428/SRR087428.fastq' | fastx_reverse_complement -Q 64 -v -o '/Volumes/Jose-Drobo/galaxy-dist/database/files/000/dataset_313.dat' galaxy.jobs.runners DEBUG 2013-10-14 14:24:32,866 executing external set_meta script for job 306: /Volumes/Jose-Drobo/galaxy-dist/set_metadata.sh ./database/files /Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306 . /Volumes/Jose-Drobo/galaxy-dist/universe_wsgi.ini /Volumes/Jose-Drobo/galaxy-dist/database/tmp/tmprYzdng /Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/galaxy.json /Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_in_HistoryDatasetAssociation_312_XtTL8q,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_kwds_HistoryDatasetAssociation_312_3MJoHa,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_out_HistoryDatasetAssociation_312_82_iZG,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_results_HistoryDatasetAssociation_312_k5blD2,,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_override_HistoryDatasetAssociation_312_tFX5kW galaxy.jobs.runners DEBUG 2013-10-14 14:24:35,692 execution of external set_meta for job 306 finished galaxy.jobs DEBUG 2013-10-14 14:24:35,781 setting dataset state to ERROR galaxy.jobs DEBUG 2013-10-14 14:24:35,949 job 306 ended Cheers Ian On Oct 14, 2013, at 12:05 PM, Dave Bouvier <d...@bx.psu.edu> wrote: > Ian, > > Although the fastx tools have been migrated to the tool shed, this migration > has not yet been released to the stable branch, but is planned to be included > in the upcoming release. In the meantime, I would suggest maintaining the > binary installation of the fastx dependencies using one of the options > described on this page: > > http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies > > After the release, you can then run the automated process to install the > migrated tools from the tool shed as described here: > > http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution > > --Dave B. > > On 10/14/2013 09:14 AM, UMD Bioinformatics wrote: >> Dave, >> >> Here is my information on the revision. >> >> $ hg heads | more >> changeset: 10421:a477486bf18e >> branch: stable >> tag: tip >> user: Nate Coraor <n...@bx.psu.edu> >> date: Thu Sep 26 11:02:58 2013 -0400 >> summary: Bugfix for tool-to-destination mapping, tool ids are lowercased >> but the mapping id was not lowercased. >> >> changeset: 10411:c42567f43aa7 >> user: greg >> date: Mon Aug 19 13:19:56 2013 -0400 >> summary: Filter invalid objects when generating the list of >> repository_dependencies objects that are associated with a tool shed >> repository installed into Galaxy. >> >> On Oct 14, 2013, at 9:11 AM, Dave Bouvier <d...@bx.psu.edu> wrote: >> >>> Ian, >>> >>> To help track down this issue, could you provide the revision of Galaxy >>> you're running? >>> >>> --Dave B. >>> >>> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote: >>>> Hello all, >>>> >>>> I'm still dealing with an error regarding Fastx toolkit. I all of the >>>> fastx commands in my /usr/local and I have installed fastx via the >>>> toolshed. I'm am still receiving the following error. Any help would be >>>> great. >>>> >>>> Cheers >>>> Ian >>>> >>>> An error occurred with this dataset://bin/sh: fasta_formatter: command >>>> not found cat: stdout: Broken pipe/ >>>> / >>>> / >>>> / >>>> / >>>> On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics >>>> <bioinformatics....@gmail.com <mailto:bioinformatics....@gmail.com>> wrote: >>>> >>>>> Bjöern, >>>>> >>>>> Here is the error message. >>>>> >>>>> An error occurred with this dataset://bin/sh: fastq_to_fasta: command >>>>> not found gzip: stdout: Broken pipe/ >>>>> / >>>>> / >>>>> / >>>>> / >>>>> On Oct 10, 2013, at 7:06 PM, Björn Grüning >>>>> <bjoern.gruen...@pharmazie.uni-freiburg.de >>>>> <mailto:bjoern.gruen...@pharmazie.uni-freiburg.de>> wrote: >>>>> >>>>>> Hi Ian, >>>>>> >>>>>> what mean broken pipe error, can you post the error message here? >>>>>> >>>>>> Thanks, >>>>>> Bjoern >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I've got a local install of galaxy with fastx tools installed. I'm >>>>>>> getting a broken pipe error but I'm not sure why. I install fastx >>>>>>> using the compiler outside galaxy and it was working fine inside >>>>>>> galaxy previously. Fastx works fine via the command line. I've >>>>>>> checked the xml files and I don't see how galaxy cannot find the >>>>>>> commands. I am running this off and external volume, but I don't >>>>>>> think that matters. >>>>>>> >>>>>>> Cheers >>>>>>> Ian >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ___________________________________________________________ >>>>>>> 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/ >>>>>> >>>>>> >>>>>> >>>>>> ___________________________________________________________ >>>>>> 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/ >>>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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/ >>>> >> >> ___________________________________________________________ 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/
