[med-svn] r12046 - in trunk/packages/qiime/trunk/debian: . patches scripts scripts/shell

[Timothy Booth]

Author: tbooth-guest
Date: 2012-08-14 16:51:24 +0000 (Tue, 14 Aug 2012)
New Revision: 12046

Modified:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/patches/series
   trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
   trunk/packages/qiime/trunk/debian/scripts/uclust
Log:
Some minor fixes, mainly due to my repackaging of rdp-classifier.


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2012-08-14 16:49:39 UTC (rev 12045)
+++ trunk/packages/qiime/trunk/debian/changelog	2012-08-14 16:51:24 UTC (rev 12046)
@@ -1,4 +1,4 @@
-qiime (1.5.0-2ubuntu2) precise; urgency=low
+qiime (1.5.0-2ubuntu4) precise; urgency=low
 
   * Remove python26_trim_sff_primers.patch as Qiime now requires 
     2.7 anyway
@@ -8,8 +8,10 @@
   * Added various symlinks as Qiime wants everything in one place
   * Set python-biom-format as a hard dependency because even built-in
     self-test won't start without it
+  * Added patch to self-test where it looks for default config file
+  * Modified to work with new RDP-classifier package
 
- -- Tim Booth <tbooth at ceh.ac.uk>  Fri, 10 Aug 2012 17:52:06 +0100
+ -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 14 Aug 2012 17:33:26 +0100
 
 qiime (1.5.0-2) unstable; urgency=low
 

Modified: trunk/packages/qiime/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series	2012-08-14 16:49:39 UTC (rev 12045)
+++ trunk/packages/qiime/trunk/debian/patches/series	2012-08-14 16:51:24 UTC (rev 12046)
@@ -1 +1,2 @@
+check_config_file_in_new_location.patch
 fix_binary_helper_location.patch

Modified: trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment	2012-08-14 16:49:39 UTC (rev 12045)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment	2012-08-14 16:51:24 UTC (rev 12046)
@@ -11,6 +11,10 @@
 export QIIME_CONFIG_FP=${QIIME_CONFIG_FP:-/etc/qiime/qiime_config}
 export BLASTMAT=${BLASTMAT:-/usr/share/ncbi/data}
 
+# This was previously set in bio-linux-rdp-classifier but can now live here
+# as the rdp-classifier package has been normalised.
+export RDP_JAR_PATH=${RDP_JAR_PATH:-/usr/share/rdp-classifier/rdp_classifier.jar}
+
 # Mike Cox reports these are wanted for Ampliconnoise
 export PYRO_LOOKUP_FILE=${PYRO_LOOKUP_FILE:-/usr/share/ampliconnoise/Data/LookUp_E123.dat}
 export SEQ_LOOKUP_FILE=${SEQ_LOOKUP_FILE:-/usr/share/ampliconnoise/Data/Tran.dat}

Modified: trunk/packages/qiime/trunk/debian/scripts/uclust
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/uclust	2012-08-14 16:49:39 UTC (rev 12045)
+++ trunk/packages/qiime/trunk/debian/scripts/uclust	2012-08-14 16:51:24 UTC (rev 12046)
@@ -20,13 +20,13 @@
     bits='32-bit'
 fi
 
-echo """\
+echo """\r\
 UClust is not freely redistributable and is thus not included in the default Qiime package.
 
 To use this feature, please go to:
     http://www.drive5.com/uclust/downloads1_2_22q.html
 
 Download the $bits binary, then:
-    sudo cp uclustq1.2.21_* /usr/local/bin/uclust
+    sudo cp uclustq1.2.22_* /usr/local/bin/uclust
     sudo chmod a+x /usr/local/bin/uclust
 """