Having bin in installation path

[jbh-cas]

We employ the conda -p option to install programs for several of us to use instead of installation in a user conda env directory. The directory in which we install is named /ccg/bin and this causes a couple of problems.

This bin in the directory path before the bin directory in the earlGrey install is replaced by the sed commands in the getRepeatMaskerFasta bash function.

Modifying them in the following way seems to work without loss of generality, original lines 91 and 96 in the earlGrey file commented:

        if [[ $(which RepeatMasker) == *"bin"* ]]; then
#               libpath="$(which RepeatMasker | sed 's|bin.*|share/RepeatMasker/Libraries/RepeatMaskerLib.h5|g')"
                libpath="$(which RepeatMasker | sed 's|bin/RepeatMasker|share/RepeatMasker/Libraries/RepeatMaskerLib.h5|')"
        else
                libpath="$(which RepeatMasker | sed 's|/[^/]*$||g')/Libraries/RepeatMaskerLib.h5"
        fi
        if [[ $(which RepeatMasker) == *"bin"* ]]; then
#               PATH=$PATH:"$(which RepeatMasker | sed 's|bin.*|share/RepeatMasker/|g')"
                PATH=$PATH:"$(which RepeatMasker | sed 's|bin/RepeatMasker|share/RepeatMasker/|')"
        fi

The same lines occur in earlGreyLibConstruct too.

Thanks for the program. Looking forward to seeing it results on a couple of Squamata genomes.

best,
Jim Henderson

[jbh-cas]

With the above sed line changes and copying the .pm files from the install share/RepeatMasker dir to the install bin/ dir, things ran to completion.