[med-svn] r2617 - trunk/community/infrastructure/getData/getData.conf.d

[plessy at alioth.debian.org]

Author: plessy
Date: 2008-11-02 08:29:39 +0000 (Sun, 02 Nov 2008)
New Revision: 2617

Modified:
   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
Log:
Correcting stupid mistakes.

 - The Blast database had the wrong format,
 - the sequences were not unzipped,
 - the configuration file was broken by a missing comma.


Modified: trunk/community/infrastructure/getData/getData.conf.d/dog.getData
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/dog.getData	2008-11-02 05:59:32 UTC (rev 2616)
+++ trunk/community/infrastructure/getData/getData.conf.d/dog.getData	2008-11-02 08:29:39 UTC (rev 2617)
@@ -3,7 +3,7 @@
 $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"
+  "source" => "ln -s /etc/getData.conf.d/dog.getData.mk Makefile ; make get unpack",
   "post-download" => "make blast"
 };
 

Modified: trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control	2008-11-02 05:59:32 UTC (rev 2616)
+++ trunk/community/infrastructure/getData/getData.conf.d/dog.getData.control	2008-11-02 08:29:39 UTC (rev 2617)
@@ -8,16 +8,9 @@
 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
+ canfam2.nhr /usr/share/genome/blast/canfam2.nhr
+ canfam2.nin /usr/share/genome/blast/canfam2.nin
+ canfam2.nsq /usr/share/genome/blast/canfam2.nsq
 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

Modified: trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk
===================================================================
--- trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk	2008-11-02 05:59:32 UTC (rev 2616)
+++ trunk/community/infrastructure/getData/getData.conf.d/dog.getData.mk	2008-11-02 08:29:39 UTC (rev 2617)
@@ -7,7 +7,7 @@
 	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
+	cat *fa | formatdb -i /dev/stdin -t CanFam2.0 -n canfam2 -p F
 
 deb:
 	equivs-build /etc/getData.conf.d/dog.getData.control