remove biohpc hardcoded path

genect_rnaseq/fpkm_subset_panel.pl

@@ -9,14 +9,14 @@ my ($genelist,$fpkm_file) = ("") x 2;
 
 GetOptions( 'g|genes=s' => \$genelist,
             'f|fpkm=s' => \$fpkm_file,
-	    'i|refinfo=s'=> \$refinfo);
+	    'i|geneinfo=s'=> \$refinfo);
 
 my $fpkm_out = $fpkm_file;
 $fpkm_out =~ s/\.fpkm.+txt/\.fpkm.capture.txt/;
 open OUT, ">$fpkm_out" or die $!;
 
 #gene_info.human.txt file is required for gene alias information
-open GENEINFO, "<$refinfo/gene_info.human.txt" or die $!;
+open GENEINFO, "<$geneinfo" or die $!;
 my %geneinfo;
 while(my $gline = <GENEINFO>){
 	chomp $gline;

genect_rnaseq/geneabundance.sh

@@ -19,6 +19,7 @@ do
         p) pair_id=$OPTARG;;
         s) stranded=$OPTARG;;
 	f) filter=$OPTARG;;
+	i) ginfo=$OPTARG;;
         h) usage;;
     esac
 done
@@ -54,6 +55,6 @@ if [[ -f $filter ]]
 then
     cd ..
     mv ${pair_id}.fpkm.txt ${prefix}.fpkm.ori.txt
-    perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter
+    perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter -i $ginfo
     mv ${prefix}.fpkm.capture.txt ${pair_id}.fpkm.txt
 fi