[med-svn] r8693 - in trunk/packages/qiime/trunk/debian/scripts: . shell

[Andreas Tille]

Author: tille
Date: 2011-11-29 09:06:11 +0000 (Tue, 29 Nov 2011)
New Revision: 8693

Modified:
   trunk/packages/qiime/trunk/debian/scripts/qiime_config
   trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment
   trunk/packages/qiime/trunk/debian/scripts/uclust
Log:
Take over changes in scripts from BioLinux branch


Modified: trunk/packages/qiime/trunk/debian/scripts/qiime_config
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/qiime_config	2011-11-29 09:04:14 UTC (rev 8692)
+++ trunk/packages/qiime/trunk/debian/scripts/qiime_config	2011-11-29 09:06:11 UTC (rev 8693)
@@ -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/trunk/debian/scripts/shell/qiime_environment
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment	2011-11-29 09:04:14 UTC (rev 8692)
+++ trunk/packages/qiime/trunk/debian/scripts/shell/qiime_environment	2011-11-29 09:06:11 UTC (rev 8693)
@@ -3,10 +3,14 @@
 
 # Qiime basic environment.  Note that sourcing this file multiple times is not idempotent 
 # and should be avoided!
-# This file needt to be readable by /bin/sh so no bash-isms allowed.
+# This file needs to be readable by /bin/sh and zsh so no bash-isms allowed.
 
-export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime:/usr/local/bioinf/denoiser/denoiser
-export PATH=$PATH:/usr/lib/qiime/bin
-export QIIME_CONFIG_FP=/etc/qiime/qiime_config
-export BLASTMAT=/usr/share/ncbi/data
+export PYTHONPATH=$PYTHONPATH/:/usr/share/pyshared/qiime
+export PATH="$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/trunk/debian/scripts/uclust
===================================================================
--- trunk/packages/qiime/trunk/debian/scripts/uclust	2011-11-29 09:04:14 UTC (rev 8692)
+++ trunk/packages/qiime/trunk/debian/scripts/uclust	2011-11-29 09:06:11 UTC (rev 8693)
@@ -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