[med-svn] r3511 - in trunk/community/infrastructure/getData: . debian getData.conf.d

[Charles Plessy]

Author: plessy
Date: 2009-06-19 12:07:16 +0000 (Fri, 19 Jun 2009)
New Revision: 3511

Added:
   trunk/community/infrastructure/getData/getData.conf.d/Ensembl_genome.mk
   trunk/community/infrastructure/getData/getData.conf.d/mouse.getData
   trunk/community/infrastructure/getData/getData.conf.d/mouse.getData.mk
Modified:
   trunk/community/infrastructure/getData/ChangeLog
   trunk/community/infrastructure/getData/debian/changelog
   trunk/community/infrastructure/getData/debian/control
Log:
Factorised code and added mouse genome.


Modified: trunk/community/infrastructure/getData/ChangeLog
===================================================================
--- trunk/community/infrastructure/getData/ChangeLog	2009-06-19 12:03:58 UTC (rev 3510)
+++ trunk/community/infrastructure/getData/ChangeLog	2009-06-19 12:07:16 UTC (rev 3511)
@@ -1,3 +1,9 @@
+2009-06-19  Charles Plessy <plessy at debian.org>
+
+    * getData.conf.d/Ensembl_genome.mk: factorises from dog.getData.mk.
+    * getData.conf.d/mouse.getData*: mouse genome build NCBIM37.54 from
+    Ensembl
+
 2009-02-19  Charles Plessy <plessy at debian.org>
 
 	* ChangeLog: Added. Let's follow the GNU coding standards.

Modified: trunk/community/infrastructure/getData/debian/changelog
===================================================================
--- trunk/community/infrastructure/getData/debian/changelog	2009-06-19 12:03:58 UTC (rev 3510)
+++ trunk/community/infrastructure/getData/debian/changelog	2009-06-19 12:07:16 UTC (rev 3511)
@@ -11,5 +11,6 @@
   * deleted debian/compat (CDBS does not need it).
   * Defautl mirror directory is /var/lib/getdata instead of
     /local/databases/mirrored.
+  * Recommends perl-doc as getData --help needs it.
 
  -- Steffen Moeller <moeller at debian.org>  Mon, 11 Feb 2008 09:58:30 +0100

Modified: trunk/community/infrastructure/getData/debian/control
===================================================================
--- trunk/community/infrastructure/getData/debian/control	2009-06-19 12:03:58 UTC (rev 3510)
+++ trunk/community/infrastructure/getData/debian/control	2009-06-19 12:07:16 UTC (rev 3511)
@@ -10,6 +10,8 @@
 Package: getdata
 Architecture: all
 Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Recommends: perl-doc
+# perl-doc is needed for getData --help.
 Description: management of external databases
  Many scientific communities share the problem of regularly
  updating external database and keeping internally created

Copied: trunk/community/infrastructure/getData/getData.conf.d/Ensembl_genome.mk (from rev 3507, trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk)
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/Ensembl_genome.mk	                        (rev 0)
+++ trunk/community/infrastructure/getData/getData.conf.d/Ensembl_genome.mk	2009-06-19 12:07:16 UTC (rev 3511)
@@ -0,0 +1,9 @@
+SHARED_WGET_OPTIONS=$(shell getData --getWgetOptions)
+
+MIRROR = ftp://ftp.ensembl.org/pub/current_fasta
+
+get:
+	wget $(SHARED_WGET_OPTIONS) $(MIRROR)/$(ORGANISM_L)/dna/$(ORGANISM).$(BUILD).dna.chromosome.*.fa.gz
+
+unpack:
+	for file in *chromosome.*.fa.gz ; do zcat $$file > `basename $$file .gz` ; done


Property changes on: trunk/community/infrastructure/getData/getData.conf.d/Ensembl_genome.mk
___________________________________________________________________
Added: svn:mergeinfo
   + 

Copied: trunk/community/infrastructure/getData/getData.conf.d/mouse.getData (from rev 3507, trunk/community/infrastructure/getData/getData.conf.d/dog.getData)
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/mouse.getData	                        (rev 0)
+++ trunk/community/infrastructure/getData/getData.conf.d/mouse.getData	2009-06-19 12:07:16 UTC (rev 3511)
@@ -0,0 +1,10 @@
+print STDERR "Reading Mus musculus configuration file\n" if $verbose;
+
+$toBeMirrored{"mouse.genome"}={
+  "name" => "mm9 – Mouse Genome Sequencing Consortium",
+  "tags" => ["mouse","genome"],
+  "source" => "make -f /etc/getData.conf.d/mouse.getData.mk get unpack",
+#  "post-download" => "make blast"
+};
+
+1;


Property changes on: trunk/community/infrastructure/getData/getData.conf.d/mouse.getData
___________________________________________________________________
Added: svn:mergeinfo
   + 

Copied: trunk/community/infrastructure/getData/getData.conf.d/mouse.getData.mk (from rev 3507, trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk)
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/mouse.getData.mk	                        (rev 0)
+++ trunk/community/infrastructure/getData/getData.conf.d/mouse.getData.mk	2009-06-19 12:07:16 UTC (rev 3511)
@@ -0,0 +1,6 @@
+ORGANISM   = Mus_musculus
+ORGANISM_L = mus_musculus
+BUILD      = NCBIM37.54
+NICKNAME   = mm9
+
+include /etc/getData.conf.d/Ensembl_genome.mk


Property changes on: trunk/community/infrastructure/getData/getData.conf.d/mouse.getData.mk
___________________________________________________________________
Added: svn:mergeinfo
   +