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Commit bf75cd9a authored by Glenn Proctor's avatar Glenn Proctor
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Added configurable load limit.

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misc-scripts/xref_projection/submit_projections.pl
+ 120
− 75
View file @ bf75cd9a
......@@ -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";
......
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