I work with Linux server and if I load by shell script module its not available.
This is shell script
source /cvmfs/software.xxxx.yyyyy/modulefiles/5.1.0/loadmodules
module add unicycler-0.5.0
module add pymol
module list
unicycler --help
This is the output (line 20 doesn't fit because here isn't qsub settings as in the original script)
Loading unicycler/0.5.0
Loading requirement: intelcdk/17.1 htslib/1.9 samtools/1.9 blast/2.7.1
bowtie2/2.3.5.1 gcc/8.3.0 glibc/2.27 spades/3.15.4 racon/1.4.3
pilon/1.22-intel-19.0.4-6enqoaq ale/1
Currently Loaded Modulefiles:
1) metabase/1 8) glibc/2.27 <aL>
2) intelcdk/17.1 <aL> 9) spades/3.15.4 <aL>
3) htslib/1.9 <aL> 10) racon/1.4.3 <aL>
4) samtools/1.9 <aL> 11) pilon/1.22-intel-19.0.4-6enqoaq <aL>
5) blast/2.7.1 <aL> 12) ale/1 <aL>
6) bowtie2/2.3.5.1 <aL> 13) unicycler/0.5.0
7) gcc/8.3.0 <aL> 14) pymol/2.3.4
Key:
<module-tag> <aL>=auto-loaded
/var/spool/pbs/mom_priv/jobs/14831393.xxxx.yyyyy.zzzz.SC: line 20: unicycler: command not found
Why do I get this error even though unicycler has been loaded?
I tried many modifications and different paths. Others modules work fine. And also if I connect to machine directly, I can reach the unicycler module but not from script.
Before running unicycler command, you can output the content of the unicycler/0.5.0 module with:
module show unicycler/0.5.0
This module should append the unicycler's bin directory to the PATH environment variable. You should find in the output of the previous command something like:
prepend-path PATH /path/to/unicycler-0.5.0/bin
If the unicycler/0.5.0 module does not alter the PATH environment variable, this is why unicycler command is not found. Module file should be updated to add binary directory to PATH.
If unicycler/0.5.0 module adds a directory to PATH, check this directory exists and contains the unicycler command