patch_Famdb

earlGrey

@@ -80,7 +80,15 @@ getRepeatMaskerFasta()
 		echo "ERROR: You have entered a species name that contains a space, please use the NCBI TaxID rather than name. E.G In place of \"Homo sapiens\" use \"9606\""
 		exit 2
 	fi
-	famdb.py -i $(which RepeatMasker | sed 's|/[^/]*$||g')/Libraries/RepeatMaskerLib.h5 families -f fasta_name --include-class-in-name -a -d $RepSpec > ${OUTDIR}/${species}_Curated_Library/${RepSpec}.RepeatMasker.lib
+	if [[ $(which RepeatMasker) == *"bin"* ]]; then
+		libpath="$(which RepeatMasker | sed 's|bin.*|share/RepeatMasker/Libraries/RepeatMaskerLib.h5|g')"
+	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')"
+	fi
+	famdb.py -i $libpath families -f fasta_name --include-class-in-name -a -d $RepSpec > ${OUTDIR}/${species}_Curated_Library/${RepSpec}.RepeatMasker.lib
 	RepSub=${OUTDIR}/${species}_Curated_Library/${RepSpec}.RepeatMasker.lib
 }