diff --git a/misc-scripts/xref_projection/submit_projections.pl b/misc-scripts/xref_projection/submit_projections.pl
index 3ccd8a9e57b44ad0895786f496fc62e67ae9f2e2..efa96fc720fdc9899a19f87bf8f5a237f13c089d 100644
--- a/misc-scripts/xref_projection/submit_projections.pl
+++ b/misc-scripts/xref_projection/submit_projections.pl
@@ -4,11 +4,11 @@ use strict;
# Remember to check/set the various config optons
# ------------------------------ config -------------------------------
-my $release = 51;
+my $release = 52;
my $base_dir = "/lustre/scratch1/ensembl/gp1/projections/";
-my $conf = "release_51.ini"; # registry config file, specifies Compara location
+my $conf = "release_52.ini"; # registry config file, specifies Compara location
# location of other databases
my $host = "ens-staging";
@@ -16,6 +16,9 @@ my $port = 3306;
my $user = "ensadmin";
my $pass = "ensembl";
+# load limit for ens-staging MySQL instance above which jobs won't be started
+my $limit = 200;
+
# -------------------------- end of config ----------------------------
# check that base directory exists
@@ -34,32 +37,42 @@ if (! -e $dir) {
# common options
my $script_opts = "-conf $conf -host $host -user $user -port $port -pass $pass -version $release -release $release -quiet";
-#my $bsub_opts = "-R'select[myens-staging<200]'";
my $bsub_opts = "";
-
-my @names_and_go = (["human", "alpaca" ],
- ["human", "armadillo" ],
- ["human", "bushbaby" ],
- ["human", "cat" ],
- ["human", "chicken" ],
- ["human", "chimp" ],
- ["human", "cow" ],
- ["human", "dog" ],
- ["human", "dolphin" ],
- ["human", "elephant" ],
- ["human", "ground_shrew" ],
- ["human", "guinea_pig" ],
- ["human", "horse" ],
- ["human", "hyrax" ],
- ["human", "kangaroo_rat" ],
- ["human", "squirrel" ],
- ["human", "tarsier" ],
- ["human", "tenrec" ],
- ["human", "tree_shrew" ],
- ["human", "western_european_hedgehog"],
- ["human", "xenopus" ],
- ["mouse", "kangaroo_rat" ],
- ["mouse", "rat" ]);
+$bsub_opts .= "-R'select[myens-staging<$limit]'";
+
+
+my @names_1_1 = (["human", "chimp" ],
+ ["human", "opossum" ],
+ ["human", "dog" ],
+ ["human", "cow" ],
+ ["human", "macaque" ],
+ ["human", "chicken" ],
+ ["human", "xenopus" ],
+ ["human", "guinea_pig" ],
+ ["human", "armadillo" ],
+ ["human", "tenrec" ],
+ ["human", "western_european_hedgehog"],
+ ["human", "cat" ],
+ ["human", "elephant" ],
+ ["human", "microbat" ],
+ ["human", "platypus" ],
+ ["human", "rabbit" ],
+ ["human", "bushbaby" ],
+ ["human", "ground_shrew" ],
+ ["human", "squirrel" ],
+ ["human", "tree_shrew" ],
+ ["human", "pika" ],
+ ["human", "mouse_lemur" ],
+ ["human", "horse" ],
+ ["human", "orang_utan" ],
+ ["human", "dolphin" ],
+ ["human", "hyrax" ],
+ ["human", "megabat" ],
+ ["human", "tarsier" ],
+ ["human", "alpaca" ],
+ ["human", "gorilla" ],
+ ["mouse", "kangaroo_rat" ],
+ ["mouse", "rat" ]);
my @names_1_many = (["human", "zebrafish" ],
["human", "medaka" ],
@@ -67,64 +80,96 @@ my @names_1_many = (["human", "zebrafish" ],
["human", "fugu" ],
["human", "stickleback"]);
-my @go_only = (["human", "mouse" ],
- ["human", "rat" ],
- ["mouse", "alpaca" ],
- ["mouse", "armadillo" ],
- ["mouse", "bushbaby" ],
- ["mouse", "cat" ],
- ["mouse", "chicken" ],
- ["mouse", "chimp" ],
- ["mouse", "cow" ],
- ["mouse", "dog" ],
- ["mouse", "dolphin" ],
- ["mouse", "elephant" ],
- ["mouse", "ground_shrew" ],
- ["mouse", "guinea_pig" ],
- ["mouse", "human" ],
- ["mouse", "hyrax" ],
- ["mouse", "kangaroo_rat" ],
- ["mouse", "macaque" ],
- ["mouse", "megabat" ],
- ["mouse", "microbat" ],
- ["mouse", "mouse_lemur" ],
- ["mouse", "opossum" ],
- ["mouse", "orang_utan" ],
- ["mouse", "pika" ],
- ["mouse", "platypus" ],
- ["mouse", "rabbit" ],
- ["mouse", "rat" ],
- ["mouse", "squirrel" ],
- ["mouse", "tarsier" ],
- ["mouse", "tenrec" ],
- ["mouse", "tree_shrew" ],
- ["mouse", "western_european_hedgehog"],
- ["mouse", "horse" ],
- ["rat", "human" ],
- ["rat", "mouse" ],
- ["drosophila", "anopheles" ],
- ["drosophila", "aedes" ],
- ["danio", "xenopus" ],
- ["danio", "fugu" ],
- ["danio", "tetraodon" ],
- ["xenopus", "danio" ]);
+my @go_terms = (["human", "mouse" ],
+ ["human", "rat" ],
+ ["human", "dog" ],
+ ["human", "chicken" ],
+ ["human", "cow" ],
+ ["human", "chimp" ],
+ ["human", "macaque" ],
+ ["human", "guinea_pig" ],
+ ["human", "bushbaby" ],
+ ["human", "rabbit" ],
+ ["human", "cat" ],
+ ["human", "ground_shrew" ],
+ ["human", "western_european_hedgehog"],
+ ["human", "microbat" ],
+ ["human", "armadillo" ],
+ ["human", "elephant" ],
+ ["human", "tenrec" ],
+ ["human", "opossum" ],
+ ["human", "platypus" ],
+ ["human", "squirrel" ],
+ ["human", "tree_shrew" ],
+ ["human", "pika" ],
+ ["human", "mouse_lemur" ],
+ ["human", "horse" ],
+ ["human", "orang_utan" ],
+ ["human", "dolphin" ],
+ ["human", "hyrax" ],
+ ["human", "megabat" ],
+ ["human", "tarsier" ],
+ ["human", "alpaca" ],
+ ["human", "kangaroo_rat" ],
+ ["human", "gorilla" ],
+ ["mouse", "human" ],
+ ["mouse", "rat" ],
+ ["mouse", "dog" ],
+ ["mouse", "chicken" ],
+ ["mouse", "cow" ],
+ ["mouse", "chimp" ],
+ ["mouse", "macaque" ],
+ ["mouse", "guinea_pig" ],
+ ["mouse", "bushbaby" ],
+ ["mouse", "rabbit" ],
+ ["mouse", "cat" ],
+ ["mouse", "ground_shrew" ],
+ ["mouse", "western_european_hedgehog"],
+ ["mouse", "microbat" ],
+ ["mouse", "armadillo" ],
+ ["mouse", "elephant" ],
+ ["mouse", "tenrec" ],
+ ["mouse", "opossum" ],
+ ["mouse", "platypus" ],
+ ["mouse", "squirrel" ],
+ ["mouse", "tree_shrew" ],
+ ["mouse", "pika" ],
+ ["mouse", "horse" ],
+ ["mouse", "orang_utan" ],
+ ["mouse", "mouse_lemur" ],
+ ["mouse", "dolphin" ],
+ ["mouse", "hyrax" ],
+ ["mouse", "megabat" ],
+ ["mouse", "tarsier" ],
+ ["mouse", "alpaca" ],
+ ["mouse", "kangaroo_rat" ],
+ ["mouse", "gorilla" ],
+ ["rat", "human" ],
+ ["rat", "mouse" ],
+ ["drosophila", "anopheles" ],
+ ["drosophila", "aedes" ],
+ ["danio", "xenopus" ],
+ ["danio", "fugu" ],
+ ["danio", "tetraodon" ],
+ ["xenopus", "danio" ]);
my ($from, $to, $o, $e, $n);
# ----------------------------------------
-# Display names and GO terms
+# Display names
-foreach my $pair (@names_and_go) {
+# 1:1
+foreach my $pair (@names_1_1) {
($from, $to) = @$pair;
$o = "$dir/names_${from}_$to.out";
$e = "$dir/names_${from}_$to.err";
$n = substr("n_${from}_$to", 0, 10); # job name display limited to 10 chars
my $all = ($from eq "human") ? "" : "--all_sources"; # non-human from species -> use all sources
- print "Submitting name and GO term projection from $from to $to\n";
- system "bsub $bsub_opts -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -names -delete_names -go_terms -delete_go_terms -no_database $all";
+ print "Submitting name projection from $from to $to\n";
+ system "bsub $bsub_opts -o $o -e $e -J $n perl project_display_xrefs.pl $script_opts -from $from -to $to -names -delete_names -no_database $all";
}
-# 1:many name projections
+# 1:many
foreach my $pair (@names_1_many) {
($from, $to) = @$pair;
$o = "$dir/names_${from}_$to.out";
@@ -135,11 +180,11 @@ foreach my $pair (@names_1_many) {
}
# ----------------------------------------
-# GO terms only
+# GO terms
$script_opts .= " -nobackup";
-foreach my $pair (@go_only) {
+foreach my $pair (@go_terms) {
($from, $to) = @$pair;
$o = "$dir/go_${from}_$to.out";
$e = "$dir/go_${from}_$to.err";