Added script (with example input) for helping with fully

automated delta building.

misc-scripts/binary_delta/databases.txt.example

+anopheles_gambiae_core_13_2
+anopheles_gambiae_core_14_2
+anopheles_gambiae_core_15_2
+anopheles_gambiae_est_13_2
+anopheles_gambiae_est_14_2
+anopheles_gambiae_est_15_2
+anopheles_gambiae_estgene_13_2
+anopheles_gambiae_estgene_14_2
+anopheles_gambiae_estgene_15_2
+anopheles_gambiae_lite_13_2
+anopheles_gambiae_lite_14_2
+anopheles_gambiae_lite_15_2
+anopheles_gambiae_snp_13_2
+anopheles_gambiae_snp_14_2
+anopheles_gambiae_snp_15_2
+caenorhabditis_briggsae_core_13_25
+caenorhabditis_briggsae_core_14_25
+caenorhabditis_briggsae_core_15_25
+caenorhabditis_briggsae_estgene_13_25
+caenorhabditis_briggsae_estgene_14_25
+caenorhabditis_briggsae_estgene_15_25
+caenorhabditis_briggsae_fasta_13_25
+caenorhabditis_briggsae_fasta_14_25
+caenorhabditis_briggsae_fasta_15_25
+caenorhabditis_briggsae_lite_13_25
+caenorhabditis_briggsae_lite_14_25
+caenorhabditis_briggsae_lite_15_25
+caenorhabditis_elegans_core_13_98
+caenorhabditis_elegans_core_14_98
+caenorhabditis_elegans_core_15_102
+caenorhabditis_elegans_lite_13_98
+caenorhabditis_elegans_lite_14_98
+caenorhabditis_elegans_lite_15_102
+danio_rerio_core_13_08
+danio_rerio_core_14_2
+danio_rerio_core_15_2
+danio_rerio_est_14_2
+danio_rerio_est_15_2
+danio_rerio_estgene_14_2
+danio_rerio_estgene_15_2
+danio_rerio_fasta_15_2
+danio_rerio_lite_13_08
+danio_rerio_lite_14_2
+danio_rerio_lite_15_2
+drosophila_melanogaster_core_13_3
+drosophila_melanogaster_core_14_3
+drosophila_melanogaster_core_15_3a
+drosophila_melanogaster_lite_13_3
+drosophila_melanogaster_lite_14_3
+drosophila_melanogaster_lite_15_3a
+ensembl_compara_13_1
+ensembl_compara_14_1
+ensembl_compara_15_1
+ensembl_family_13_1
+ensembl_family_14_1
+ensembl_family_15_1
+ensembl_go_13_1
+ensembl_go_14_1
+ensembl_go_15_1
+ensembl_mart_13_1
+ensembl_mart_14_1
+ensembl_mart_15_1
+fugu_rubripes_core_13_2
+fugu_rubripes_core_14_2
+fugu_rubripes_core_15_2
+fugu_rubripes_fasta_15_2
+fugu_rubripes_lite_13_2
+fugu_rubripes_lite_14_2
+fugu_rubripes_lite_15_2
+homo_sapiens_core_13_31
+homo_sapiens_core_14_31
+homo_sapiens_core_15_33
+homo_sapiens_disease_13_31
+homo_sapiens_disease_14_31
+homo_sapiens_disease_15_33
+homo_sapiens_est_13_31
+homo_sapiens_est_14_31
+homo_sapiens_est_15_33
+homo_sapiens_estgene_13_31
+homo_sapiens_estgene_14_31
+homo_sapiens_estgene_15_33
+homo_sapiens_fasta_13_31
+homo_sapiens_fasta_14_31
+homo_sapiens_fasta_15_33
+homo_sapiens_haplotype_13_31
+homo_sapiens_haplotype_14_31
+homo_sapiens_haplotype_15_33
+homo_sapiens_lite_13_31
+homo_sapiens_lite_14_31
+homo_sapiens_lite_15_33
+homo_sapiens_snp_13_31
+homo_sapiens_snp_14_31
+homo_sapiens_snp_15_33
+homo_sapiens_vega_13_31
+homo_sapiens_vega_14_31
+homo_sapiens_vega_15_33
+mus_musculus_core_13_30
+mus_musculus_core_14_30
+mus_musculus_core_15_30
+mus_musculus_est_13_30
+mus_musculus_est_14_30
+mus_musculus_est_15_30
+mus_musculus_estgene_13_30
+mus_musculus_estgene_14_30
+mus_musculus_estgene_15_30
+mus_musculus_fasta_13_30
+mus_musculus_fasta_14_30
+mus_musculus_fasta_15_30
+mus_musculus_lite_13_30
+mus_musculus_lite_14_30
+mus_musculus_lite_15_30
+mus_musculus_snp_13_30
+mus_musculus_snp_14_30
+mus_musculus_snp_15_30
+rattus_norvegicus_core_13_2
+rattus_norvegicus_core_14_2
+rattus_norvegicus_core_15_2
+rattus_norvegicus_est_13_2
+rattus_norvegicus_est_14_2
+rattus_norvegicus_est_15_2
+rattus_norvegicus_estgene_13_2
+rattus_norvegicus_estgene_14_2
+rattus_norvegicus_estgene_15_2
+rattus_norvegicus_fasta_13_2
+rattus_norvegicus_fasta_14_2
+rattus_norvegicus_fasta_15_2
+rattus_norvegicus_lite_13_2
+rattus_norvegicus_lite_14_2
+rattus_norvegicus_lite_15_2
+rattus_norvegicus_snp_13_2
+rattus_norvegicus_snp_14_2
+rattus_norvegicus_snp_15_2

misc-scripts/binary_delta/planner.pl

+#!/usr/bin/perl -w
+
+# $Id$
+#
+# Don't use this program unless you know exactly what you and it
+# are doing!
+#
+# Use like this:
+#
+#   planner.pl <databases.txt >do_it_all.sh
+#
+# Please take a look at the whole of "do_it_all.sh" before
+# running it!  It assumes that the current directory contains
+# certain directories and files, it removes files, and it
+# contains no safty catches whatsoever.
+#
+# See "databases.txt.example" for an example of "databases.txt".
+#
+# Author: Andreas Kahari, <andreas.kahari@ebi.ac.uk>
+#
+
+use strict;
+use warnings;
+
+my %thing;
+
+while (defined(my $line = <>)) {
+    chomp $line;
+
+    $line =~ /^(.*)_([1-9][0-9]*_[0-9]*[a-z]?)$/;
+    if (!defined($1) || !defined($2) || $1 eq "" || $2 eq "") {
+	printf STDERR "Problems: %s\n", $line;
+	die;	# FIXME:  Doesn't catch everything...
+    }
+    my $db = $1;
+    my $v  = $2;
+
+    push @{ $thing{$db} }, $v;
+}
+
+my @work;
+foreach my $db (keys %thing) {
+    foreach my $v (@{ $thing{$db} }) {
+	print <<EOT;
+scp -c none -r ecs3:/mysqla/current/var/${db}_$v databases/
+EOT
+    }
+
+    for (my $i = 0; $i < scalar @{ $thing{$db} } - 1; ++$i) {
+	print <<EOT;
+perl ./build.pl -c ./xdelta.osf -s databases -d deltas \\
+   $db $thing{$db}[$i] $thing{$db}[$i + 1] | \\
+   tee deltas/${db}_$thing{$db}[$i]_delta_$thing{$db}[$i + 1].txt
+EOT
+    }
+
+    foreach my $v (@{ $thing{$db} }) {
+	print <<EOT;
+rm -rf databases/${db}_$v
+EOT
+    }
+}