src/hg/encode/encodeLoad/doEncodeLoad.pl 1.72
1.72 2010/03/15 22:21:53 krish
added script to generate changes notes for ENCODE tracks
Index: src/hg/encode/encodeLoad/doEncodeLoad.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeLoad/doEncodeLoad.pl,v
retrieving revision 1.71
retrieving revision 1.72
diff -b -B -U 4 -r1.71 -r1.72
--- src/hg/encode/encodeLoad/doEncodeLoad.pl 6 Oct 2009 00:52:26 -0000 1.71
+++ src/hg/encode/encodeLoad/doEncodeLoad.pl 15 Mar 2010 22:21:53 -0000 1.72
@@ -1,12 +1,11 @@
#!/usr/bin/env perl
-# encodeLoad.pl - load ENCODE data submission generated by the
-# automated submission pipeline
-# Reads load.ra for information about what to do
+# encodeLoad.pl - load ENCODE data submission generated by the automated
+# submission pipeline Reads load.ra for information about what to do
-# Writes error or log information to STDOUT
-# Returns 0 if load succeeds and sends email to wrangler for lab specified in the DAF
+# Writes error or log information to STDOUT Returns 0 if load succeeds and
+# sends email to wrangler for lab specified in the DAF
# DO NOT EDIT the /cluster/bin/scripts copy of this file --
# edit the CVS'ed source at:
# $Header$
@@ -144,12 +143,15 @@
my $safe = SafePipe->new(CMDS => \@cmds, STDOUT => "/dev/null", STDERR => $stderrFile, DEBUG => $opt_debug);
if(my $err = $safe->exec()) {
print STDERR "ERROR: File(s) $fileList failed wiggle load:\n\n";
dieFile($stderrFile);
- } elsif (system("rm -f /gbdb/$assembly/wib/$tableName.wib") ||
- system("ln -s $submitPath/$tableName.wib /gbdb/$assembly/wib")) {
+ }
+
+ if (system("rm -f /gbdb/$assembly/wib/$tableName.wib") ||
+ system("ln -s $gbdbDir/$tableName.wib /gbdb/$assembly/wib")) {
die("ERROR: failed wiggle load ln\n");
- } else {
+ }
+
print "$fileList loaded into $tableName\n";
# retrieve lower and upper limits from $stderrFile and fix-up trackDb.ra file to add this to wig type line
my $lines = Encode::readFile($stderrFile);
@@ -163,9 +165,8 @@
!system($cmd) || die "trackDb.ra update failed: $?\n";
}
}
}
- }
push(@{$pushQ->{TABLES}}, $tableName);
push(@{$pushQ->{FILES}}, "$submitPath/$tableName.wib");
}
@@ -320,8 +321,9 @@
}
} else {
$configPath = "$submitDir/../config"
}
+print $configPath, "\n";
my $grants = Encode::getGrants($configPath);
my $fields = Encode::getFields($configPath);
my $daf = Encode::getDaf($submitDir, $grants, $fields);
@@ -366,9 +368,9 @@
}
if(!(-e $unloader)) {
die "Can't find unloader ($unloader)\n";
}
- if(system("$unloader $submitType $submitPath")) {
+ if(system("$unloader -configDir $configPath $submitType $submitPath")) {
die "unload script failed\n";
}
#TODO change to : FileUtils.cp $loadRa, $unloadRa
@@ -393,15 +395,15 @@
HgAutomate::verbose(2, "loadRa ($loadRa) has: " . scalar(keys %ra) . " records\n");
my $compositeTrack = Encode::compositeTrackName($daf);
my $downloadDir = Encode::downloadDir($daf);
+my $gbdbDir = Encode::gbdbDir($daf);
+
+# make the download dir if it doesn't exist
if(!$opt_skipDownload and !(-d $downloadDir)) {
- # Change of plans: simlink to /cluster/data/encode/pipeline/downloads
- if(!(-d "/cluster/data/encode/pipeline/downloads/$compositeTrack")) {
- mkdir "/cluster/data/encode/pipeline/downloads/$compositeTrack" || die ("Can't create download directory (error: '$!'); please contact your wrangler at: $email\n");
+ if(!(-d $downloadDir)) {
+ mkdir $downloadDir || die ("Can't create download directory (error: '$!'); please contact your wrangler at: $email\n");
}
- !system("/bin/ln -s /cluster/data/encode/pipeline/downloads/$compositeTrack $downloadDir") || die ("Can't link to download directory (error: '$!'); please contact your wrangler at: $email\n");
- #mkdir $downloadDir || die ("Can't create download directory (error: '$!'); please contact your wrangler at: $email\n");
}
for my $key (keys %ra) {
my $h = $ra{$key};
@@ -477,9 +479,9 @@
if (! -d "$downloadDir/raw") {
mkdir "$downloadDir/raw" or die "Could not create dir [$downloadDir/raw] error: [$!]\n";
}
}
- $target =~ s/ //g; # removes space in ".bed 6.gz" for example
+ $target =~ s/ //g; # removes space in ".bed 5.gz" for example
unlink($target);
HgAutomate::verbose(2, "unlink($target)\n");
if(@files == 1) {
@@ -569,27 +571,27 @@
UNLOCK TABLES;
_EOF_
close(PUSHQ);
-if(-e $readmeFile) {
- open(README, ">>$readmeFile") || die "SYS ERROR: Can't write '$readmeFile' file; error: $!\n";
- print README "\n";
-} else {
- open(README, ">$readmeFile") || die "SYS ERROR: Can't write '$readmeFile' file; error: $!\n";
- print README <<END;
-This directory contains data generated by the $daf->{grant}/$daf->{lab} lab
-as part of the Encode project.
-
-Data is RESTRICTED FROM USE in publication until the restriction date
-noted for the given data file. See the ENCODE
-data release policy at:
-
-http://genome.ucsc.edu/encodeDCC/ENCODE_Consortia_Data_Release_Policy_2008-09-11.doc
-
-Files included in this directory:
-
-END
-}
+#if(-e $readmeFile) {
+# open(README, ">>$readmeFile") || die "SYS ERROR: Can't write '$readmeFile' file; error: $!\n";
+# print README "\n";
+#} else {
+# open(README, ">$readmeFile") || die "SYS ERROR: Can't write '$readmeFile' file; error: $!\n";
+# print README <<END;
+#This directory contains data generated by the $daf->{grant}/$daf->{lab} lab
+#as part of the Encode project.
+#
+#Data is RESTRICTED FROM USE in publication until the restriction date
+#noted for the given data file. See the ENCODE
+#data release policy at:
+#
+#http://genome.ucsc.edu/encodeDCC/ENCODE_Consortia_Data_Release_Policy_2008-09-11.doc
+#
+#Files included in this directory:
+#
+#END
+#}
if(! -e $preambleFile ) {
open(PREAMBLE, ">$preambleFile") || die "SYS ERROR: Can't write '$preambleFile' file; error: $!\n";
# NOTE: can remove the CHANGE-ME comment if we switch to SSI for the hostname