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:

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":

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:

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?


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