[med-svn] r8407 - in trunk/packages/qiime/branches/lucid/debian: . patches scripts scripts/shell

Timothy Booth tbooth-guest at alioth.debian.org
Fri Nov 4 12:29:52 UTC 2011 

Author: tbooth-guest
Date: 2011-11-04 12:29:51 +0000 (Fri, 04 Nov 2011)
New Revision: 8407

Modified:
   trunk/packages/qiime/branches/lucid/debian/changelog
   trunk/packages/qiime/branches/lucid/debian/control
   trunk/packages/qiime/branches/lucid/debian/patches/series
   trunk/packages/qiime/branches/lucid/debian/rules
   trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config
   trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment
   trunk/packages/qiime/branches/lucid/debian/scripts/uclust
Log:
Some small fixes to Qiime including environment settings to pick up helper
tools.  Everything apart from the changelog and rules file should probably be
pushed to the Debian package too.


Modified: trunk/packages/qiime/branches/lucid/debian/changelog
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/changelog	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/changelog	2011-11-04 12:29:51 UTC (rev 8407)
@@ -1,10 +1,9 @@
-qiime (1.3.0-1) unstable; urgency=low
+qiime (1.3.0-0ubuntu6) lucid; urgency=low
 
-  * Bringing qiime to Debian
-  [Steffen]
-  * Some reformatting of debian/control
+  * Attempt to fix some errors reported by print_qiime_config -t
+    Fixes to environment, configuration and small patches 
 
- -- Tim Booth <tbooth at ceh.ac.uk>  Fri, 26 Aug 2011 17:48:30 +0200
+ -- Tim Booth <tbooth at ceh.ac.uk>  Wed, 02 Nov 2011 18:06:37 +0000
 
 qiime (1.3.0-0ubuntu5) lucid; urgency=low
 

Modified: trunk/packages/qiime/branches/lucid/debian/control
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/control	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/control	2011-11-04 12:29:51 UTC (rev 8407)
@@ -5,7 +5,7 @@
 Uploaders: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
 Build-Depends: debhelper (>= 8), cdbs, python, python-central, python-cogent ( >= 1.5.1 ), python-numpy, python-matplotlib, ghc6
 Standards-Version: 3.9.2
-Homepage: http://qiime.sourceforge.net/
+Homepage: http://www.qiime.org/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/
 XS-Python-Version: >= 2.6

Modified: trunk/packages/qiime/branches/lucid/debian/patches/series
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/patches/series	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/patches/series	2011-11-04 12:29:51 UTC (rev 8407)
@@ -1,2 +1,3 @@
 python26_trim_sff_primers.patch
 fix_shebang_lines.patch
+fix_binary_helper_location.patch

Modified: trunk/packages/qiime/branches/lucid/debian/rules
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/rules	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/rules	2011-11-04 12:29:51 UTC (rev 8407)
@@ -27,7 +27,7 @@
 # Python scripts go into /usr/lib/qiime/bin (not /usr/bin)
 # Helper script goes into /usr/bin
 # Setup scripts go into /usr/lib/qiime/shell
-# Default configuration goes into /etc/qiime/default_qiime_config
+# Default configuration goes into /etc/qiime/qiime_config
 # ...or maybe it should be copied to $HOME/.qiime_config on 1st run?
 # Since 3.0, denoiser is aliased to Qiime
 common-binary-fixup-arch::
@@ -47,3 +47,4 @@
 	( cd $(ROOTDIR)/usr/share/doc/`dh_listpackages` ; mv ChangeLog.gz changelog.gz || true )
 	# And about the existence of /usr/qiime
 	mv $(ROOTDIR)/usr/qiime/support_files $(ROOTDIR)/usr/lib/qiime && rmdir $(ROOTDIR)/usr/qiime
+

Modified: trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/qiime_config	2011-11-04 12:29:51 UTC (rev 8407)
@@ -8,7 +8,6 @@
 working_dir	.
 blastmat_dir	/usr/share/ncbi/data
 blastall_fp	blastall
-rdp_classifier_fp 
 pynast_template_alignment_fp
 pynast_template_alignment_blastdb
 template_alignment_lanemask_fp
@@ -16,4 +15,3 @@
 seconds_to_sleep	60
 qiime_scripts_dir	/usr/lib/qiime/bin/
 temp_dir	/tmp
-pyronoise_data_fp	/usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat

Modified: trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/shell/qiime_environment	2011-11-04 12:29:51 UTC (rev 8407)
@@ -6,7 +6,11 @@
 # This file needs to be readable by /bin/sh and zsh so no bash-isms allowed.
 
 export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime
-export PATH=$PATH:/usr/lib/qiime/bin
-export QIIME_CONFIG_FP=/etc/qiime/qiime_config
-export BLASTMAT=/usr/share/ncbi/data
+export PATH="$PATH:/usr/lib/qiime/bin:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer"
 export QIIME_HELP_TEXT=/usr/lib/qiime/shell/qiime_help
+export QIIME_CONFIG_FP=${QIIME_CONFIG_FP:-/etc/qiime/qiime_config}
+export BLASTMAT=${BLASTMAT:-/usr/share/ncbi/data}
+
+# Mike Cox reports these are wanted for Ampliconnoise
+export PYRO_LOOKUP_FILE=${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/branches/lucid/debian/scripts/uclust
===================================================================
--- trunk/packages/qiime/branches/lucid/debian/scripts/uclust	2011-11-04 04:05:17 UTC (rev 8406)
+++ trunk/packages/qiime/branches/lucid/debian/scripts/uclust	2011-11-04 12:29:51 UTC (rev 8407)
@@ -24,7 +24,7 @@
 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_21q.html
+    http://www.drive5.com/uclust/downloads1_2_22q.html
 
 Download the $bits binary, then:
     sudo cp uclustq1.2.21_* /usr/local/bin/uclust

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