Smalle bug fix

diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm
index ad243995e20e8e0c2efb44b6296caa171b266e99..3c6b9c51f832babdba5ff61221434448e657e0e2 100755 (executable)
--- a/htswanalysis/scripts/ConfigureTasks.pm
+++ b/htswanalysis/scripts/ConfigureTasks.pm
@@ -19,6 +19,7 @@ my $CmdQueue = Thread::Queue->new;
 
 my $root_dir = shift;
 my $data_dir = shift;
+my $parm = shift;
 
 my %libs;
 
@@ -27,15 +28,20 @@ my $QUESTDIR = "$root_dir/bin/QuEST/QuEST_ver_0.3";
 my $MACSDIR  = "$root_dir/bin/MACS/bin";
 my $WINGPEAKSDIR = "$root_dir/bin/WingPeaks/bin";
 my $WINGPEAKSGENOMEDIR = "$root_dir/bin/WingPeaks/genome_cod";
-my $PROFILEDIR = "$root_dir/bin/profile_reads";
+my $PROFILEDIR = "$root_dir/bin/";
 my $GENOMEDIR = "/Volumes/Genomes";
-my $QPCRDIR = "$root_dir/bin/qPCR";
+my $QPCRDIR = "$root_dir/bin/";
 my $QPCRTESTDIR = "$root_dir/reference_data/qPCR_Tests";
 my $QPCRBACKGROUND = "$root_dir/reference_data/GenericBackground";
 
 my $SUMMARIZE_PROJECT="$root_dir/scripts/SummarizeProject2.pm";
 
-my $parm = shift;
+###
+### Check directory for project and task folders. Make them if necessary
+### May not have permissions for this. These should be moved to an install script
+`if [ ! -e $data_dir/Tasks ]; then mkdir $data_dir/Tasks; fi;`;
+`if [ ! -e $data_dir/Projects ]; then mkdir $data_dir/Projects; fi;`;
+
 
 ###
 ### Important: get the xml file form the server.
@@ -82,7 +88,7 @@ print STDERR "Task makefile complete\n";
 my $index_list = "";
 for(split(/ /,$projects)) { $index_list .= "$_/index.html "; }
 
-open(MAKE,">ProjectMakefile");
+open(MAKE,">$data_dir/Projects/ProjectMakefile");
 print MAKE "all: $index_list | .start\n\n.PHONY: $index_list .start\n\n.start:\n\ttouch .start; echo \"Projects updated at `date`\";\n\n$index_list:\n\t".'cd `dirname $@` && $SUMMARIZE_PROJECT ../../LibraryInfo.xml > `basename $@`'."\n";
 close(MAKE);
 
@@ -109,12 +115,12 @@ sub writeProject {
   my @tasks = split(/ /,$tasks);
 
   if(! (-e $projectdir && -d $projectdir)) {
-    `mkdir $projectdir`;
+    `mkdir $data_dir/Projects/$projectdir`;
   }
 
   print STDERR "Created directory $projectdir\n";
 
-  $xmldoc->XMLout($project, OutputFile=>"$projectdir/Project.xml", RootName=>"Project", XMLDecl=>1);
+  $xmldoc->XMLout($project, OutputFile=>"$data_dir/Projects/Project.xml", RootName=>"Project", XMLDecl=>1);
 
   print STDERR "Wrote configureation for project $projectdir\n";
 
@@ -134,7 +140,7 @@ sub writeTask {
   my $cmd = shift;
 
   my $taskid = $task->{TaskId};
-  my $taskdir = "../Tasks/".$taskid;
+  my $taskdir = "$data_dir/Tasks/".$taskid;
 
   if(! (-e $taskdir && -d $taskdir)) {
     `mkdir $taskdir`;
@@ -146,7 +152,7 @@ sub writeTask {
   print MAKEFILE "all: .notify $outfile | .start\n\n.PHONY: .notify .start\n\n";
   print MAKEFILE ".start:\n\t$root_dir/scripts/analys_track_main.py updsts $taskid \"Processing\"\n\ttouch .start\n\n";
   
-  print MAKEFILE ".notify: | .start $outfile .start\n\techo \"Complete\"\n\t$root_dit/scripts/analys_track_main.py updsts $taskid \"Complete\"\n\ttouch .notify\n\n";
+  print MAKEFILE ".notify: | .start $outfile .start\n\techo \"Complete\"\n\t$root_dir/scripts/analys_track_main.py updsts $taskid \"Complete\"\n\ttouch .notify\n\n";
   print MAKEFILE "$cmd";
   close(MAKEFILE);
   registerTask($taskid);