[med-svn] r13837 - trunk/packages/microbiomeutil/trunk/debian

[Timothy Booth]

Author: tbooth-guest
Date: 2013-06-05 12:14:06 +0000 (Wed, 05 Jun 2013)
New Revision: 13837

Modified:
   trunk/packages/microbiomeutil/trunk/debian/changelog
   trunk/packages/microbiomeutil/trunk/debian/control
   trunk/packages/microbiomeutil/trunk/debian/rules
Log:
Pre-compute some necessary index files (ChimeraSlayer would do this anyway on the
first run if it could write to the relevant dir)

Please fold my latest changelog entry into the entry for -3


Modified: trunk/packages/microbiomeutil/trunk/debian/changelog
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/changelog	2013-06-05 08:14:33 UTC (rev 13836)
+++ trunk/packages/microbiomeutil/trunk/debian/changelog	2013-06-05 12:14:06 UTC (rev 13837)
@@ -1,3 +1,12 @@
+microbiomeutil (20101212-1ubuntu8) precise; urgency=low
+
+  * Bio-Linux rebuild with Andreas' fixes  
+  * ChimeraSlayer run from QIIME was not working.  Need to pre-compute
+    index files and add them to RESOURCES directory
+  * Also added missing direct dep on blast2
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Wed, 05 Jun 2013 12:50:22 +0100
+
 microbiomeutil (20101212-2) unstable; urgency=low
 
   * Initial release to Debian (Closes: #711086)

Modified: trunk/packages/microbiomeutil/trunk/debian/control
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/control	2013-06-05 08:14:33 UTC (rev 13836)
+++ trunk/packages/microbiomeutil/trunk/debian/control	2013-06-05 12:14:06 UTC (rev 13837)
@@ -6,7 +6,8 @@
            Tim Booth <tbooth at ceh.ac.uk>,
            Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 9),
-               cdbfasta
+               cdbfasta,
+               blast2
 Standards-Version: 3.9.4
 Homepage: http://microbiomeutil.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/microbiomeutil/trunk/
@@ -31,7 +32,8 @@
 Architecture: all
 Depends: ${misc:Depends},
          microbiomeutil-data,
-         cdbfasta
+         cdbfasta,
+         blast2
 Recommends: nast-ier
 Description: detects likely chimeras in PCR amplified DNA
  ChimeraSlayer is a chimeric sequence detection utility, compatible with

Modified: trunk/packages/microbiomeutil/trunk/debian/rules
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/rules	2013-06-05 08:14:33 UTC (rev 13836)
+++ trunk/packages/microbiomeutil/trunk/debian/rules	2013-06-05 12:14:06 UTC (rev 13837)
@@ -11,6 +11,18 @@
 override_dh_auto_test :
 	true
 
+override_dh_auto_build :
+	dh_auto_build
+	#Pre-make indexes for ChimeraSlayer, otherwise it tries to write them
+	#to the non-writeable dir on first run and blows up
+	formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null
+	cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
+
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx
+	rm -f formatdb.log
+
 override_dh_install:
 	dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c