Thanks Youri,

That's the bit of code I was worrying about (BAM grooming). I've filed an
issue for this:

https://github.com/galaxyproject/galaxy/issues/1336

Peter


On Wed, Dec 16, 2015 at 9:47 AM, Y. Hoogstrate <y.hoogstr...@erasmusmc.nl>
wrote:

> Great news Peter,
>
> This is how Galaxy seems to do it:
>
>         command = "samtools sort %s %s" % ( file_name,
> tmp_sorted_dataset_file_name_prefix )
>         proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir,
> stderr=open( stderr_name, 'wb' ) )
>
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L278
>
>
> Since galaxy ships with a builtin pysam (0.8.3) wheel, I think it would be
> handier to use pysam for sorting (once updated to the latest HTSlib).
> Pysam now also has all samtools c functions directly builtin:
>
> pysam.index( "arg1", "arg2" ) is the equivalent of the command line
> argument *samtools index "arg1" "arg2"*
>
> ...
>
Youri
>
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