Author: plessy
Date: 2008-11-02 05:59:32 +0000 (Sun, 02 Nov 2008)
New Revision: 2616
Added:
trunk/community/infrastructure/getData/getData.conf.d/dog.getData
trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control
trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk
Modified:
trunk/community/infrastructure/getData/getData
Log:
Exploring the possibility of using makefiles:
- Added an command to ast getData what wget option it uses.
- Added a getData configuration file to download the dog genome.
- Added a makefile that does the work.
- Added a control file to build a package containing a dog genome
BLAST database with equivs.
Modified: trunk/community/infrastructure/getData/getData
===================================================================
--- trunk/community/infrastructure/getData/getData 2008-11-02 03:55:53 UTC
(rev 2615)
+++ trunk/community/infrastructure/getData/getData 2008-11-02 05:59:32 UTC
(rev 2616)
@@ -16,7 +16,7 @@
# astronomy.
# Copyright (c) 2008 Steffen Moeller <[EMAIL PROTECTED]>
-# Copyright (c) 2008 Charles Plessy <[EMAIL PROTECTED]>
+# Copyright (c) 2008 Charles Plessy <[EMAIL PROTECTED]>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
@@ -240,6 +240,10 @@
This information is not used at the moment, also to render this script
more useful for other Linux distributions than Debian.
+=item getWgetOptions - private command to get wget options
+
+This is used at download time by makefiles and is not intended to be used
interactively.
+
=back
@@ -463,7 +467,7 @@
$mirrordir = "/var/lib/mirrored" unless defined($mirrordir);
$confd = "/etc/getData.conf.d" unless defined($confd);
-my
($post,$source,$removal,$config,$list,$help,$man,$verbose)=(undef,undef,undef,0,0,0,0);
+my
($post,$source,$removal,$config,$list,$help,$man,$verbose,$getWgetOptions)=(undef,undef,undef,0,0,0,0,0);
my %options=("mirrordir:s" => \$mirrordir,
"list" => \$list,
@@ -473,7 +477,8 @@
"confd=s"=>\$confd,
"config:s@"=>\$config,
"remove"=>\$removal,
- "source"=>\$source);
+ "source"=>\$source,
+ "getWgetOptions"=>\$getWgetOptions);
my ($do_source,$do_post,$do_config,$do_removal)=(1,1,0,0);
@@ -495,6 +500,10 @@
myhelp()
}
+if ($getWgetOptions) {
+ die ("$sharedWgetOptions\n");
+}
+
print "post: $post, source: $source\n" if $verbose;
if ($post) {
@@ -536,7 +545,7 @@
}
if ( -d "$confd" ) {
- foreach my $f (glob "$confd/*") {
+ foreach my $f (glob "$confd/*.getData") {
eval require $f or die "Could not read '$f': [EMAIL PROTECTED]";
print STDERR "Read '$f'\n";
}
Added: trunk/community/infrastructure/getData/getData.conf.d/dog.getData
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/dog.getData
(rev 0)
+++ trunk/community/infrastructure/getData/getData.conf.d/dog.getData
2008-11-02 05:59:32 UTC (rev 2616)
@@ -0,0 +1,10 @@
+print STDERR "Reading Canis lupus familiaris configuration file\n";
+
+$toBeMirrored{"dog.genome"}={
+ "name" => "CanFam2.0 - Dog Genome Sequencing Project",
+ "tags" => ["dog","genome"],
+ "source" => "ln -s /etc/getData.conf.d/dog.getData.mk Makefile ; make get"
+ "post-download" => "make blast"
+};
+
+1;
Added: trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control
(rev 0)
+++ trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control
2008-11-02 05:59:32 UTC (rev 2616)
@@ -0,0 +1,24 @@
+Section: genome
+Priority: optional
+Standards-Version: 3.6.2
+
+Package: dog-genome-blast
+Version: CanFam2.0-1
+Maintainer: Charles Plessy <[EMAIL PROTECTED]>
+Recommends: blast2
+Architecture: all
+Files:
+ canfam2.00.phr /usr/share/genome/blast/canfam2.00.phr
+ canfam2.00.pin /usr/share/genome/blast/canfam2.00.pin
+ canfam2.00.psq /usr/share/genome/blast/canfam2.00.psq
+ canfam2.01.phr /usr/share/genome/blast/canfam2.01.phr
+ canfam2.01.pin /usr/share/genome/blast/canfam2.01.pin
+ canfam2.01.psq /usr/share/genome/blast/canfam2.01.psq
+ canfam2.02.phr /usr/share/genome/blast/canfam2.02.phr
+ canfam2.02.pin /usr/share/genome/blast/canfam2.02.pin
+ canfam2.02.psq /usr/share/genome/blast/canfam2.02.psq
+ canfam2.pal /usr/share/genome/blast/canfam2.pal
+Description: The dog genome indexed for NCBI blast.
+ This is a completely experimental packages with no guaratee at all.
+ Please do not use it yet if you find it by chance, it is not intended
+ to be released for the moment.
Added: trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk
(rev 0)
+++ trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk
2008-11-02 05:59:32 UTC (rev 2616)
@@ -0,0 +1,13 @@
+SHARED_WGET_OPTIONS=$(shell getData --getWgetOptions)
+
+get:
+ wget $SHARED_WGET_OPTIONS
ftp://ftp.ensembl.org/pub/current_fasta/canis_familiaris/dna/Canis_familiaris.BROADD2.50.dna.chromosome.*.fa.gz
+
+unpack:
+ for file in *chromosome.*.fa.gz ; do zcat $$file > `basename $$file
.gz` ; done
+
+blast:
+ cat *fa | formatdb -i /dev/stdin -t CanFam2.0 -n canfam2
+
+deb:
+ equivs-build /etc/getData.conf.d/dog.getData.control
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