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#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/lib/qiime/support_files/denoiser/bin/FlowgramAli_4frame"
export PATH="$PATH:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer"
export QIIME_HELP_TEXT=/usr/lib/qiime/shell/qiime_help
export QIIME_CONFIG_FP=${QIIME_CONFIG_FP:-/etc/qiime/qiime_config}
export BLASTMAT=${BLASTMAT:-/usr/share/ncbi/data}
# This was previously set in bio-linux-rdp-classifier but can now live here
# as the rdp-classifier package has been normalised.
export RDP_JAR_PATH=${RDP_JAR_PATH:-/usr/share/rdp-classifier/rdp_classifier.jar}
#RDP_classifier is very bad at admitting what version it is, so ask DPKG:
export RDP_JAR_VERSION_OK=`dpkg-query -f '${Version}\n' -W rdp-classifier | sed 's/[~+-].*//'`
# Mike Cox reports these are wanted for Ampliconnoise
export PYRO_LOOKUP_FILE=${PYRO_LOOKUP_FILE:-/usr/share/ampliconnoise/Data/LookUp_E123.dat}
export SEQ_LOOKUP_FILE=${SEQ_LOOKUP_FILE:-/usr/share/ampliconnoise/Data/Tran.dat}
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