Hi Ross,

I tried installing again it shows no item..

Also i couldn't find any .log  file or the (
/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix) in the tool dependency
directory.

Thanks


On Wed, Aug 21, 2013 at 12:13 PM, Ross <ross.laza...@gmail.com> wrote:

> 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 <
> sridhar2bioi...@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.laza...@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 <
>>> 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
>>>>>>>> >
>>>>>>>> > ________________________________________________
>>>>>>>
>>>>>>>
>
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