Currently, when samtools is not in the PATH, the hisatgenotype script runs to completion but without any output or obvious error messages.
This PR adds a check to ensure that samtools is in the PATH when the hisatgenotype script is run.
Note that this is separated from the samtools check in the setup.sh script as that checks when that script is run (https://github.com/DaehwanKimLab/hisat-genotype/pull/31). It's conceived that samtools was available at that time (e.g. through a conda environment), but then when an end-user runs hisatgenotype they forgot to activate this same environment (I did this by accident). This PR makes sure that the program fails fast so that end-users can be notified right away.
Currently, when
samtoolsis not in the PATH, thehisatgenotypescript runs to completion but without any output or obvious error messages.This PR adds a check to ensure that
samtoolsis in the PATH when thehisatgenotypescript is run.Note that this is separated from the samtools check in the
setup.shscript as that checks when that script is run (https://github.com/DaehwanKimLab/hisat-genotype/pull/31). It's conceived that samtools was available at that time (e.g. through a conda environment), but then when an end-user runs hisatgenotype they forgot to activate this same environment (I did this by accident). This PR makes sure that the program fails fast so that end-users can be notified right away.