Sridhar, Kindly try rerunning the failed job to confirm that it still fails now that the tool installation should have well and truly finished - it does take a while. If it still fails the same way, please send me a copy of the installation log for the htseq dependency found in: [your tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan < sridhar2bioinfo@gmail.com> wrote:
Hi Ross,
i Installed through admin interface . for pysam and freetype it showed new... and rest installed..
Thanks
On Wed, Aug 21, 2013 at 11:47 AM, Ross <ross.lazarus@gmail.com> wrote:
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 NameRevisionOwner Installation 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 < sridhar2bioinfo@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.mirmomeni@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 < sridhar2bioinfo@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.mirmomeni@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.gruening@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 > > > > ________________________________________________