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
Name	Revision	Owner	Installation status
package_numpy_1_7	af9633757cf0	blankenberg	Installed
package_pysam_0_7_5	a4e35f23093f	fubar	Installed
package_freetype_2_4	4e54e357ac25	bgruening	Installed
package_matplotlib_lite	8df6bbf48c3a	fubar	Installed

Installed tool dependencies - click the name to browse the dependency installation directory
Name	Version	Type	Installation status
freetype	2.4.11	package
matplotliblite	1.2.1	package
numpy	1.7.1	package
pysam	0.7.5	package
htseq	0.5.4p3	package

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
>

> ________________________________________________