Re: [galaxy-dev] Samtools and idxstats
On Mon, Nov 11, 2013 at 5:29 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 7, 2013 at 4:51 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Michiel, Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed... If not, I may tackle this shortly. Peter I've implemented a 'samtools idxstats' wrapper, which seems to be working for me: https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Main Tool Shed (pending - I want to see the overnight test results on the Test Tool Shed first): http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Having sorted out the dependency management, and seen the test pass on the Test Tool Shed, this samtools idxstats wrapper is now live on the main Tool Shed as well: http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Peter ___ 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/
Re: [galaxy-dev] Samtools and idxstats
On Thu, Nov 7, 2013 at 4:51 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Michiel, Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed... If not, I may tackle this shortly. Peter I've implemented a 'samtools idxstats' wrapper, which seems to be working for me: https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Main Tool Shed (pending - I want to see the overnight test results on the Test Tool Shed first): http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Regards, Peter ___ 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/
Re: [galaxy-dev] Samtools and idxstats
Hi Michiel,
Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...
If not, I may tackle this shortly.
Peter
On Wed, May 22, 2013 at 2:39 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper like this (assuming the name of your input dataset is 'input_bam':
${input_bam.metadata.bam_index}
Once you have the file path, you can set up a symbolic link to it and the
tool should work fine.
Good luck,
J.
On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
Hi,
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code, which
led me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently relies
on having an index file available (within the same directory) for the bam
file you which to print the stats for.
E.g. samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai and gives an error when this file is not
present. And somehow I cannot model this behavior in Galaxy.
A different solution would of course be to ask the author(s) of samtools to
have an option available where the user can directly indicate the path to
the index file.
regards,
Michiel
PS: I've searched the mailing list archives for this problem but did not
find any matches. Apologies if I somehow missed the answer.
___
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[galaxy-dev] Samtools and idxstats
Hi, I would like to inquire whether anyone has attempted to implement the idxstats tool from samtools into Galaxy? The xml-file for idxstats is not present in the Galaxy source code, which led me to try and implement it myself. However, the main problem I face is that the idxstats tool silently relies on having an index file available (within the same directory) for the bam file you which to print the stats for. E.g. samtools idxstats PATH/test.bam searches for PATH/test.bam.bai and gives an error when this file is not present. And somehow I cannot model this behavior in Galaxy. A different solution would of course be to ask the author(s) of samtools to have an option available where the user can directly indicate the path to the index file. regards, Michiel PS: I've searched the mailing list archives for this problem but did not find any matches. Apologies if I somehow missed the answer. -- == Michiel Van Bel, PhD Expert Bioinformatician Tel:+32 (0)9 331 36 95fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mi...@psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be == ___ 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/
Re: [galaxy-dev] Samtools and idxstats
Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper like this (assuming the name of your input dataset is 'input_bam':
${input_bam.metadata.bam_index}
Once you have the file path, you can set up a symbolic link to it and the tool
should work fine.
Good luck,
J.
On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
Hi,
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code, which led
me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently relies on
having an index file available (within the same directory) for the bam file
you which to print the stats for.
E.g. samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai and gives an error when this file is not
present. And somehow I cannot model this behavior in Galaxy.
A different solution would of course be to ask the author(s) of samtools to
have an option available where the user can directly indicate the path to the
index file.
regards,
Michiel
PS: I've searched the mailing list archives for this problem but did not find
any matches. Apologies if I somehow missed the answer.
--
==
Michiel Van Bel, PhD
Expert Bioinformatician
Tel:+32 (0)9 331 36 95fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mi...@psb.vib-ugent.be http://www.psb.vib-ugent.be
http://bioinformatics.psb.ugent.be
==
___
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___
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