Meta-script to ease submitting of the various xref projections to the farm.

misc-scripts/xref_projection/submit_projections.pl

+use strict;
+
+# Submits the display name and GO term projections as farm jobs
+# Remember to check/set the various config optons
+
+# ------------------------------ config -------------------------------
+my $release = 43;
+
+my $base_dir = "/lustre/work1/ensembl/gp1/projections/";
+
+my $conf = "release_43.conf"; # registry config file, relative to cwd
+
+my $compara = "compara_43"; # name in registry file
+
+# -------------------------- end of config ----------------------------
+
+# check that base directory exists
+die ("Cannot find base directory $base_dir") if (! -e $base_dir);
+
+# create release subdir if necessary
+my $dir = $base_dir. $release;
+if (! -e $dir) {
+  mkdir $dir;
+  print "Created $dir\n";
+} else {
+  print "Cleaning and re-using $dir\n";
+  unlink <$dir/*.out>, <$dir/*.err>;
+}
+
+# common options
+my $opts = "-conf $conf -compara $compara -release $release";
+
+my ($o, $e);
+
+# ----------------------------------------
+# Display names
+
+# human to chimp,opossum,dog,cow,macaque,chicken,xenopus
+foreach my $to ("chimp", "opossum", "dog", "cow", "macaque", "chicken", "xenopus") {
+  $o = "$dir/names_human_$to.out";
+  $e = "$dir/names_human_$to.err";
+  system "bsub -o $o -e $e perl project_display_xrefs.pl $opts -from human -to $to -names -delete_names";
+}
+
+# mouse to rat
+foreach my $to ("rat") { # don't need the loop but may add more species later
+  $o = "$dir/names_mouse_$to.out";
+  $e = "$dir/names_mouse_$to.err";
+  system "bsub -o $o -e $e perl project_display_xrefs.pl $opts -from human -to $to -names -delete_names";
+}
+
+# ----------------------------------------
+# GO terms
+
+$opts .= " -nobackup";
+
+# human to mouse, rat, dog, chicken, cow
+foreach my $to ("mouse", "rat", "dog", "chicken", "cow") {
+  $o = "$dir/go_human_$to.out";
+  $e = "$dir/go_human_$to.err";
+  system "bsub -o $o -e $e perl project_display_xrefs.pl $opts -from human -to $to -go_terms -delete_go_terms";
+}
+
+# mouse to human, rat, dog, chicken, cow
+# note need to not use -delete the second time around
+foreach my $to ("human", "rat", "dog", "chicken", "cow") {
+  $o = "$dir/go_mouse_$to.out";
+  $e = "$dir/go_mouse_$to.err";
+  system "bsub -o $o -e $e perl project_display_xrefs.pl $opts -from mouse -to $to -go_terms";
+}