Peter,

For the automated indexing of bam files, Galaxy uses the samtools version linked to as "default" under tool-dependencies/samtools/

This should normally be 0.1.19 or older, due to the not-yet-implemented handling of bam_index_build and other potential regressions that could be uncovered in the future.

   --Dave B.

On 11/03/2014 01:52 PM, Peter Cock wrote:
Hello all,

Galaxy currently requires samtools on the $PATH in order to sort
and index BAM files automatically, and samtools 0.1.19 works fine.

Unfortunately later versions of samtools index have a regression:
https://github.com/samtools/samtools/issues/199

This has caught several people out already,
e.g. https://biostar.usegalaxy.org/p/7928/
and https://biostar.usegalaxy.org/p/9335/

While eventually samtools will be fixed, right now this means we
can't have samtools 1.1 as the first samtools on the $PATH used
by Galaxy.

I am working on a wrapper for "samtools bam2fq":
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq

The bam2qf command in samtools 0.1.19 has a number of bugs,
so I want to target samtools 1.1.  However this has complicated my
testing since for my BAM input files Galaxy will call "samtools index",
and if it calls samtools 1.1 this will fail.

I'm not using the tool shed dependencies during development
so instead came up with the following hack:
https://github.com/peterjc/picobio/blob/master/sambam/samtools_auto.py

My question is, what is expected to happen with a Tool Shed installed
wrapper for samtools 1.1 and Galaxy's attempts to automatically call
samtools to index any BAM output file? Would the tool environment
put samtools 1.1 on the (local) $PATH which would then break setting
the metadata as part of the same job?

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/

___________________________________________________________
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/

Reply via email to