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
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