LSF is not able to find samtools in the path you are sourcing by the samtools-1.2 command. Make sure the directory where you "installed" samtools-1.2 is appended to your $PATH (examine by)
. Also go into that directory and make sure the samtools binary is executable. If it is not, then change permissions to make it executable.
Code:
$ echo $PATH
Code:
$ chmod u+x samtools
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