[med-svn] r2616 - in trunk/community/infrastructure/getData: . getData.conf.d

[plessy at alioth.debian.org]

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 <moeller at debian.org>
-# Copyright (c) 2008 Charles Plessy <debian-no-spam at plessy.org>
+# Copyright (c) 2008 Charles Plessy <plessy at debian.org>
 # 
 # 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': $@\n";
 		print STDERR "Read '$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 <plessy at debian.org>
+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