Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar
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/
One and two way GLM with DESeq2, edgeR and VOOM are all available for brave beta testers in the differential_count_models<http://testtoolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?sort=name&operation=view_or_manage_repository&id=347ec9acdc3b02e8> tool in the statistics section of the test toolshed. Be warned, the tool takes at least 15-20 minutes to install - be patient and it should work. Suggested improvements and bug reports welcomed. 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
___________________________________________________________ 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
Sure .. Thanks for the reply.. On Tue, Aug 20, 2013 at 12:33 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
___________________________________________________________ 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/
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
___________________________________________________________ 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/
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
___________________________________________________________ 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/
Sridhar, If you read the tool form help text for the differential count tool, you will have noticed that right at the top, it says: "Requires a count matrix as a tabular file. These are best made using the companion HTSeq based counter Galaxy wrapper and your fave gene model to generate inputs....." My hope was that anyone reading that hint might realise that "companion HTSeq based counter Galaxy wrapper" meant they should go take a look in the same place for something with htseq in the name from the same author. It seems that I need some assistance to make the wording even more clear - suggestions will be appreciated. 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
___________________________________________________________ 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
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
___________________________________________________________ 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/
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
___________________________________________________________ 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/
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 < 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
___________________________________________________________ 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
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 > > ___________________________________________________________ > 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
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 > > > > ________________________________________________
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.lazarus@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 < 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 >> > >> > ________________________________________________ > >
Sridhar, Tool shed installations always create those log files, even when they fail. I am unable to offer any further assistance without seeing the installation log for the dependency. What does: find [your tool dependency directory] -name "INSTALLATION.log" show? If necessary, try navigating through the tool page in your admin interface. The htseq dependency will contain the installation log I need to see. On Wed, Aug 21, 2013 at 5:06 PM, Sridhar Srinivasan < sridhar2bioinfo@gmail.com> wrote:
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.lazarus@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 < 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 >>> > >>> > ________________________________________________ >> >>
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
participants (4)
-
Bjoern Gruening -
Mahtab Mirmomeni -
Ross -
Sridhar Srinivasan