File: qiime_environment

package info (click to toggle)
qiime 1.4.0-2
  • links: PTS, VCS
  • area: main
  • in suites: wheezy
  • size: 29,704 kB
  • sloc: python: 77,837; haskell: 379; sh: 113; makefile: 103
file content (16 lines) | stat: -rw-r--r-- 936 bytes parent folder | download 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
 
#In the /usr/lib/qiime/shell directory are .zshrc and .bashrc files to set up the environment 
#needed for running Qiime.  There may be a less hacky way of doing this but it works for now.

# Qiime basic environment.  Note that sourcing this file multiple times is not idempotent 
# and should be avoided!
# 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:/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}