samtools hard-coded to a gsc-specific path

[dy7t]

Both cobbler.pl & RAILS define SAMPATH to be "/gsc/btl/linuxbrew/bin/samtools"

The readme doesn't mention that it needs to be changed or that RAILS depends on samtools (any particular version?)

Without a valid samtools, the tests fail with:
Empty arrayn -- maybe the scaffold merging step did not necessitate
gap filling. at /group/bioinfo/apps/apps/RAILS_v1.4/RAILS line 215.
RAILS process terminated.

Consider checking that a valid samtools is present and print clear error message if its missing.

This bug was opened and then closed as fixed, but nothing seems to have changed.

I was using version 1.4

[warrenlr]

Ok, I have removed the hardcoded paths from both scripts (RAILS v1.4.1 and cobbler v0.5) and added clarity to error message.

We have been using samtools v1.8 on our end. Let me know how it goes.
thx
Rene

[mmokrejs]

Rene,
please drop the ../ from bin/runRAILS.sh as well. Also the line export PATH=/gsc/btl/linuxbrew/bin:$PATH. These are awkward. Please instruct users in Readme.md to provide samtools and your scripts via PATH. That is enough.

[mmokrejs]

The hardcoded PATHs are still present in bin/*.sh files. Also cmdline options to pass number of threads would be helpful.

[warrenlr]

done.