Sridhar, The error message you provide suggests that the HTSeq python module is not available when Galaxy tries to run the tool. Please confirm that you installed that tool through the admin interface from the test toolshed and that the admin interface for toolshed installed tools shows the installed repository in your Galaxy instance has the htseq dependency successfully installed like the end of the page below :
- Repository Actions Installed tool shed repository 'htseq_bams_to_count_matrix' Tool shed:testtoolshed.g2.bx.psu.edu Name:htseq_bams_to_count_matrix Description: Revision:f69b55c71ae5 Owner:fubar Location:/mnt/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix Deleted:False Dependencies of this repository Installed repository dependencies NameRevisionOwnerInstallation statuspackage_numpy_1_7<http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5> af9633757cf0blankenbergInstalledpackage_pysam_0_7_5<http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0> a4e35f23093ffubarInstalledpackage_freetype_2_4<http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063> 4e54e357ac25bgrueningInstalledpackage_matplotlib_lite<http://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3> 8df6bbf48c3afubarInstalled Installed tool dependencies* - click the name to browse the dependency installation directory* NameVersionTypeInstallation statusfreetype<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=148934b1ed5706b5> 2.4.11packagematplotliblite<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=dee0124e4d3ab063> 1.2.1packagenumpy<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=94e61e06dbd29e52> 1.7.1packagepysam<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=c32939704028ccc3> 0.7.5packagehtseq<http://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52&id=96c0d701aac155a0> 0.5.4p3package On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan < sridhar2bioi...@gmail.com> wrote: > Hi All, > > I installed the toolshed htseq_bams_to_count_matrix repository , i gave > the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count > reads over from your current history: in this section and all bam files. > > it gives error as " > empty > format: tabular, database: hg19 > Traceback (most recent call last): File "/data/galaxy/shed_tools/ > testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py", > line 45, in <module> import HTSeq.scripts.count as htcount " > > Thanks > > > > > On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni < > m.mirmom...@student.unimelb.edu.au> wrote: > >> You can use htseq_bams_to_count_matrix repository by fubar in the test >> toolshed. >> >> >> On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan < >> sridhar2bioi...@gmail.com> wrote: >> >>> Hi All, >>> >>> Thanks for the suggestions. I installed the Toolshed ( >>> Differential_Count (version 0.21) ). It asks for the input matrix - rows >>> are contigs, columns are counts for each sample. >>> Any idea on how to generate this matrix file?? >>> >>> Thanks >>> >>> >>> On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni < >>> m.mirmom...@student.unimelb.edu.au> wrote: >>> >>>> Hi Sridhar, >>>> >>>> I'm using differential_count_model repository by fubar in the test >>>> toolshed which has both EdgeR and Deseq2 and it's working for me. >>>> >>>> Thanks >>>> Mahtab >>>> >>>> >>>> On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening < >>>> bjoern.gruen...@gmail.com> wrote: >>>> >>>>> Hi Sridhar, >>>>> >>>>> we are developing a DESeq2 tool at the moment, if you want to join get >>>>> in touch with me. Its developed here: >>>>> >>>>> https://github.com/bgruening/galaxytools/tree/master/deseq2 >>>>> >>>>> I will upload our latest progress during the day. >>>>> Cheers, >>>>> Bjoern >>>>> >>>>> > Dear users, >>>>> > >>>>> > >>>>> > Could anybody suggest the valid DESeq toolshed for RNA sequencing??? >>>>> > >>>>> > >>>>> > Thanks >>>>> > Sridhar >>>>> > >>>>> > ___________________________________________________________ >>>>> > 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/ > -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
___________________________________________________________ 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/
