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/
