change version 1.1 to 1.1.1 and check permisson before adding symlink…

… to edge_ui/JBrowse/data

README.md

@@ -1,6 +1,6 @@
 # EDGE Bioinformatics
 
-This is version 1.1 of EDGE Bioinformatics, a product of Los Alamos National Laboratory, Naval Medical Research Center, and the Defense Threat Reduction Agency.
+This is version 1.1.1 of EDGE Bioinformatics, a product of Los Alamos National Laboratory, Naval Medical Research Center, and the Defense Threat Reduction Agency.
 
 EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data. The bioinformatics platform allows users to address a wide range of use cases including assay validation and the characterization of novel biological threats, clinical samples, and complex environmental samples.
 

runPipeline

@@ -18,7 +18,7 @@ $ENV{HOME} ||= $RealBin;
 
 # unbuffer
 $|=1;
-my $version="1.1";
+my $version="1.1.1";
 my $debug=0;
 my @unpairedReadsFile;
 my @pairedReadsFile;
@@ -2816,7 +2816,7 @@ sub writeJBrowseInfo
     my $cmd="$RealBin/scripts/edge2jbrowse_converter.pl --in-ref-fa '$referenceGenome' --in-ctg-fa $contig_for_annotation_file --in-ctg-anno-gff3 '$annoationGFF' --in-ref-gff3 '$gff3File' --proj_outdir '$abs_outDir' 2>\&1 1>$log";
     &lprint (" Running \n $cmd\n");
     &executeCommand("$cmd"); 
-    &executeCommand("ln -sf $abs_outDir $RealBin/edge_ui/JBrowse/data/$project_name") if (! -e  "$RealBin/edge_ui/JBrowse/data/$project_name");
+    &executeCommand("ln -sf $abs_outDir $RealBin/edge_ui/JBrowse/data/$project_name") if (! -e  "$RealBin/edge_ui/JBrowse/data/$project_name" && -w "$RealBin/edge_ui/JBrowse/data");
     &printRunTime($time);
     system("touch $outputDir/writeJBrowseInfo.finished");
     #return \%project;