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.profile
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.profile
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#.profile
# Set the users environment variables
#-------------------------#
# ENVIRONMENT - LOCALE #
#-------------------------#
export LC_ALL="en_US.UTF-8"
export LC_CTYPE="$LC_ALL"
export LC_COLLATE="$LC_ALL"
#-----------------------------#
# ENVIRONMENT - APPLICATIONS #
#-----------------------------#
#export LESSOPEN="|lesspipe.sh %s"
export LESS="-i -M -R -W -S -x4"
export PAGER=less
export GREP_COLOR=31
#export GREP_OPTIONS="--color=always"
export NOSPLASH=1
export NOWELCOME=1
export EDITOR=vim VISUAL=vim
export IGNOREEOF=2
#------------------------------#
# usepackage derived variables #
#------------------------------#
# use GLOBAL
export HOST="`uname -n`"
export GLOBAL_PATH=/usr/local/global.files
export PRINTER="`cat ${HOME}/.defaultprinter`"
export WWW_HOME="http://www.jcvi.org"
export TITLE="${USER}@$HOST%"
export OSVERSION="`uname -r`"
export RELEASE="`uname -r`"
export MACHINE="`uname -n`"
export RSYNC_RSH="ssh"
# PREFIX_PATH
#PREFIX_PATH=/home/vkrishna
# local/packages
PACKAGES=/usr/local/packages
# use ANNOTATION_ENV
export ANNOTATION_DIR=/usr/local/annotation
# use EGC
export ANNOT_DEVEL=/usr/local/devel/ANNOTATION
export EGC_UTILITIES=${ANNOT_DEVEL}/EGC_utilities/bin
export EGC_SCRIPTS=${ANNOT_DEVEL}/vkrishna/euk_genome_control
export EUK_MODULES=${ANNOT_DEVEL}/vkrishna/Euk_modules
export EUK_ORGANIZATION=${ANNOT_DEVEL}/vkrishna/EUK_ORGANIZATION
# JCVI projects area
export PROJECTS=/usr/local/projdata
# Medicago/Annotation specific
export MTG_PCODE=0372
export LEG_PCODE=0689
#export MTG3=${PROJECTS}/${MTG_PCODE}/projects/MTG3
export MTG4=${PROJECTS}/${MTG_PCODE}/projects/MTG4
export CURRENT=${MTG4}/A17/Current_annotation
#export MTA4=/usr/local/annotation/MTA4
export LEGUME=${PROJECTS}/${LEG_PCODE}/projects/LEGUME
# Other annotation projects
#export BOG=${PROJECTS}/BOG
#export WILLOW=${PROJECTS}/WILLOW
#export GBROWSE=${ANNOT_DEVEL}/vkrishna/GBrowse
# AIP specific paths
export AIP_PCODE=0611
export AIP=${PROJECTS}/${AIP_PCODE}/projects/AIP
#source $AIP/DataProviders/TAIR/araport.env
# machtype
export MACHTYPE="x86_64"
# Amazon EC2 Private Key
export EC2_PRIVATE_KEY=${MTG4}/Workshop2014/AWS/jcvi_workshop_2014-$USER.pem
# PASA
export PASAHOME=${AIP}/local/packages/PASA
export PASA_HOME=$PASAHOME
# Trinity
export TRINITY_HOME=${AIP}/local/packages/trinityrnaseq
# JBrowse
export JBROWSE=${MTG4}/packages/JBrowse-current
# NCBI-BLAST+
export BLASTPLUS=${PACKAGES}/ncbi-blast+
# MAKER HOME
export MAKER_HOME=${AIP}/local/packages/maker
export MPICH_HOME=${AIP}/local/packages/mpich-install
# BEDTOOLS
export BEDTOOLS=${PACKAGES}/bedtools
# AUGUSTUS
export AUGUSTUS_CONFIG_PATH=${PACKAGES}/augustus/config
# PATH
RPATH="${HOME}/bin|/opt/real/RealPlayer|/usr/local/bin|/usr/local/sbin"
PATH=$( echo ${PATH} | tr -s ":" "\n" | grep -vwE "(${RPATH})" | tr -s "\n" ":" | sed "s/:$//" )
if [[ "${HOSTNAME}" == "itchy" ]]; then
## itchy.jcvi.org specific configuration for BISQUE
export BQROOT=/opt/www/maize-bisque
#export BQVERSION="bisque-053"
PATH=/opt/software/php/bin:/opt/www/MTGD/drush:${BQROOT}/bin:/usr/local/bin:/usr/local/sbin:${PATH}:${HOME}/bin
LD_LIBRARY_PATH=${PACKAGES}/postgresql/lib:${PACKAGES}/percona-server/lib:${BQROOT}/lib:${PACKAGES}/fftw/lib:${PACKAGES}/gcc/lib64:${PACKAGES}/python/lib:/usr/local/lib64:${HOME}/lib
PKG_CONFIG_PATH=${BQROOT}/lib/pkgconfig
PYTHONPATH=${BQROOT}/lib/python2.7/site-packages
HDF5_DIR=/usr/local/packages/hdf5
elif [[ "${HOSTNAME}" == "columbia" ]]; then
PATH=/opt/admin/bin:${AIP}/bin:${AIP}/local/bin:/opt/www/araport/bin:/usr/local/bin:/usr/local/sbin:${HOME}/bin:${PATH}:/usr/local/projects/AIP/vkrishna/git/foundation-cli/bin
LD_LIBRARY_PATH=${AIP}/local/lib:/opt/www/araport/lib:${PACKAGES}/postgresql/lib:${PACKAGES}/gcc/lib64:${PACKAGES}/python/lib:/usr/local/lib:${HOME}/lib
PYTHONPATH=${AIP}/vkrishna/git:${PACKAGES}/python/lib/python2.7/site-packages:${HOME}/lib/python2.7/site-packages
PERL5LIB=/opt/www/araport/lib:${AIP}/local/lib
else
# PATH
PATH=${BEDTOOLS}/bin:${MAKER_HOME}/bin:${MPICH_HOME}/bin:${BLASTPLUS}/bin:${MTG4}/local/bin:${AIP}/bin:${AIP}/local/bin:/export/apache2/bin:/export/php/bin:/export/bin:${HOME}/.gem/ruby/1.9.1/bin:${HOME}/bin/eval:${HOME}/bin/icommands:${HOME}/.perl-shell:${HOME}/bin/${MACHTYPE}:${HOME}/.local/bin:${HOME}/bin:${EGC_SCRIPTS}:${EGC_UTILITIES}:${EUK_MODULES}:/usr/local/bin:/usr/local/sbin:/usr/local/genome/bin:/usr/local/common:${PATH}:/usr/local/projects/AIP/vkrishna/git/foundation-cli/bin
PATH=${PATH}:/home/sgeworker/bin:/usr/sbin:/sbin:/opt/real/RealPlayer
# LD_LIBRARY_PATH
LD_LIBRARY_PATH=${PACKAGES}/postgresql/lib:${PACKAGES}/percona-server/lib:${MTG4}/local/lib:${AIP}/local/lib:/export/lib:${PACKAGES}/gcc/lib64:${PACKAGES}/samtools/lib:${PACKAGES}/bzip2/lib:${PACKAGES}/python/lib:${PACKAGES}/atlas/lib:${PACKAGES}/boost/lib:${PACKAGES}/sybase/OCS/lib:/usr/local/lib:${HOME}/lib:/usr/lib64
# PYTHONPATH
PYTHONPATH=${AIP}/vkrishna/git:${AIP}/local/lib/python2.7/site-packages:${HOME}/.local/lib/python2.7/site-packages:${PACKAGES}/python/lib/python2.7/site-packages:${HOME}/lib/python2.7/site-packages:${MTG4}/packages/clean_reads
# clean_reads and seq_crumbs
CLEAN_READS=${MTG4}/packages/clean_reads
SEQ_CRUMBS=${MTG4}/packages/seq_crumbs
# PERL5LIB
#PERL5LIB=${HOME}/lib:${HOME}/lib/eval:${HOME}/git.local/jcvi/db/lib:${EUK_MODULES}:${EGC_SCRIPTS}
PERL5LIB=${MTG4}/local/lib:${AIP}/local/lib:${HOME}/git.local/jcvi/db/lib:${EUK_MODULES}:${EGC_SCRIPTS}
# PKG_CONFIG_PATH
PKG_CONFIG_PATH=/usr/lib/pkgconfig:${PACKAGES}/glib/lib/pkgconfig
# ANT_HOME and ANT_OPTS
export ANT_HOME=${AIP}/local/packages/apache-ant
export ANT_OPTS="-server -XX:MaxPermSize=256M -Xmx6g -XX:+UseParallelGC -Xms1700m -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99"
PATH=${ANT_HOME}/bin:${PATH}
## CHADO
export GMOD_ROOT=${MTG4}/vkrishna/gmod
export CHADO_DB_NAME=chadotest1
export CHADO_DB_USERNAME=vkrishna
export CHADO_DB_PASSWORD=vkrishna9
export CHADO_DB_HOST=localhost
export CHADO_DB_PORT=5432
fi
PKG_CONFIG_PATH=$PKG_CONFIG_PATH:${HOME}/lib/pkgconfig
export PATH LD_LIBRARY_PATH PYTHONPATH PKG_CONFIG_PATH PERL5LIB
# use phred
export PHRED_PARAMETER_FILE=/usr/local/etc/PhredPar/phredpar.dat
# use tmake
export TMAKEPATH=${PACKAGES}/tmake/lib/linux-g++
# use polybaye
export POLYBAYES_LIB=${PACKAGES}/PolyBayes_3_0/lib
# use cvs
export CVSROOT=":ext:${USER}@cvs.jcvi.org:/usr/local/src/cvsroot"
# use sybase
export SYBASE=${PACKAGES}/sybase
export LANG="en_US.UTF-8"
export DSQUERY="SYBPROD"
# EVM
export EVM=${ANNOT_DEVEL}/EVidenceModeler
# use hmm
export HMMER_NCPU="1"
export HMM_SCRIPTS=${ANNOT_DEVEL}/hmm/bin
# InterProScan
export IPRSCAN_HOME=${ANNOT_DEVEL}/iprscan/iprscan_v4.7
export IPRSCAN_LIB=${IPRSCAN_HOME}/lib
# AAT
export AATPATH=/usr/local/bin
export SVNHOME="http://isvn.tigr.org/ANNOTATION"
export TZ="EST5EDT"
export LOGNAME="vkrishna"
# CURL
export CURL_LIBS=${PACKAGES}/curl/lib
export CURL_CFLAGS=${PACKAGES}/curl/include
# BOOST libs
export BOOST_ROOT=${PACKAGES}/boost
# OPENMP thread number
export OMP_NUM_THREADS=64
# MYSQL
export MYSQLINC=${PACKAGES}/percona-server/include/mysql
export MYSQLLIBS="${PACKAGES}/percona-server/lib/mysql/libperconaserverclient.a -lz"
# NCBI
export TBL2ASN=/usr/local/packages/tbl2asn/bin
export ASNDISC=/usr/local/packages/asndisc/bin
export ASNVAL=/usr/local/packages/asnval/bin
export SEQUIN=/usr/local/packages/sequin
export PATH=${TBL2ASN}:${ASNDISC}:${ASNVAL}:${SEQUIN}:$PATH
# ADAMA env variables
export ARAPORT=https://api.araport.org
export ADAMA=$ARAPORT/community/v0.3
# use shell
ulimit -s unlimited >& /dev/null
ulimit -Sc 0 >& /dev/null
umask 002
# Import custom ENV
export PCODE="0372"
export EMAIL="vkrishna@jcvi.org"
SGE=/usr/local/sge_current/jcvi/common/settings.sh
WORKFLOW=${ANNOT_DEVEL}/workflow-3.1.3/exec_env.bash
JAVA160=/usr/local/common/env/java6.sh
#JAVA170=/usr/local/common/env/java7.sh
JAVA170=${HOME}/env/java7.sh
GITCOMP=${HOME}/.git-completion.bash
GITPROMPT=${HOME}/.git-prompt.sh
ICMDS=${HOME}/.i-commands-auto.bash
declare -a ENVVARS=(SGE WORKFLOW JAVA170 GITCOMP GITPROMPT ICMDS)
for i in ${ENVVARS[@]}; do
eval ENVVAR=\$$i
if [ -r "$ENVVAR" ]; then
if [ "$PS1" ]; then
. "$ENVVAR"
else
. "$ENVVAR" >/dev/null 2>&1
fi
fi
done
# LinuxBrew
export PATH="$HOME/.linuxbrew/bin:$PATH"
export MANPATH="$HOME/.linuxbrew/share/man:$MANPATH"
export INFOPATH="$HOME/.linuxbrew/share/info:$INFOPATH"
# MANPATH
MANPATH=${HOME}/share/man:/usr/local/common/man:${MANPATH}
MANPATH=${MANPATH}:/usr/man:/usr/X11R6/man:/opt/gnome/share/man:/usr/openwin/man
export MANPATH
# enable autojump
[[ -s /home/vkrishna/.autojump/etc/profile.d/autojump.sh ]] && source /home/vkrishna/.autojump/etc/profile.d/autojump.sh
# setting required for GPG
export GPG_TTY=$(tty)
#-------------------------#
# SHELL - CHECK TYPE #
#-------------------------#
#[[ $- != *i* ]] && return