Merge pull request #103 from TobyBaril/102-bug-when-using-soft-link-t…

…o-genome

102 bug when using soft link to genome

README.md

@@ -169,13 +169,13 @@ If you would like to try Earl Grey, or prefer to use it in a browser, you can do
 
 NOTE: This pipeline is currently running with Dfam 3.7 curated elements only. We are working on updating to Dfam 3.8 for a future release. If required, you can modify the conda installation of RepeatMasker within the conda environment (do at your own risk!)
 
-Earl Grey version 4.2.1 (pre-release) with all required and configured dependencies is found in the `toby_baril_bio` conda channel. To install, simply run the following depending on your installation:
+Earl Grey version 4.2.2 (pre-release) with all required and configured dependencies is found in the `toby_baril_bio` conda channel. To install, simply run the following depending on your installation:
 ```
 # With conda
-conda create -n earlgrey -c conda-forge -c bioconda -c toby_baril_bio earlgrey=4.2.1
+conda create -n earlgrey -c conda-forge -c bioconda -c toby_baril_bio earlgrey=4.2.2
 
 # With mamba
-mamba create -n earlgrey -c conda-forge -c bioconda -c toby_baril_bio earlgrey=4.2.1
+mamba create -n earlgrey -c conda-forge -c bioconda -c toby_baril_bio earlgrey=4.2.2
 ```
 
 Earl Grey version 4.1.1 with all required and configured dependencies is found in the bioconda channel. To install, simply run the following depending on your installation:

earlGrey

@@ -3,7 +3,7 @@
 usage()
 {
 	echo "	#############################
-	earlGrey version 4.2.0
+	earlGrey version 4.2.2
 	Required Parameters:
 		-g == genome.fasta
 		-s == species name
@@ -56,6 +56,9 @@ prepGenome()
 	if [ ! -L ${genome} ]; then
 		genome=$(realpath ${genome})
 	fi
+	if [ -L $genome ]; then
+		genome=$(realpath -s ${genome})
+	fi
 	if [ ! -f ${genome}.prep ] || [ ! -f ${genome}.dict ]; then
 		cp ${genome} ${genome}.bak && gzip -f ${genome}.bak 
 		sed '/>/ s/ .*//g; /^$/d' ${genome} > ${genome}.tmp