sourceme.csh

#
# Copyright (c) 2017 10x Genomics, Inc. All rights reserved.
#
# Environment setup for package cellranger-2.1.1.
# Source this file before running.
#

set SOURCE=($_)
if ( "$SOURCE" != "" ) then
    set SOURCE=`readlink -f "$SOURCE[2]"`
else
    set SOURCE=`readlink -f "$0"`
endif
set DIR=`dirname $SOURCE`

#
# Source user's own environment first.
#
# Note .login is for login shells only.
source ~/.cshrc

#
# Modify the prompt to indicate user is in 10X environment.
#


#
# Set aside environment variables if they may conflict with 10X environment
#

if ( ! $?_TENX_LD_LIBRARY_PATH ) then
    setenv _TENX_LD_LIBRARY_PATH "$LD_LIBRARY_PATH"
    setenv LD_LIBRARY_PATH ""
endif


#
# Unset environment variables if they may conflict with 10X environment
#

if ( $?PYTHONPATH ) then
    unsetenv PYTHONPATH
endif


#
# Add module binary paths to PATH
#

if ( ! $?PATH ) then
    setenv PATH "$DIR/STAR/5dda596"
else
    setenv PATH "$DIR/STAR/5dda596:$PATH"
endif
setenv PATH "$DIR/martian-cs/2.3.2/bin:$PATH"
setenv PATH "$DIR/lz4/v1.8.0:$PATH"
setenv PATH "$DIR/cellranger-cs/2.1.1/bin:$PATH"
setenv PATH "$DIR/cellranger-cs/2.1.1/tenkit/bin:$PATH"
setenv PATH "$DIR/cellranger-cs/2.1.1/tenkit/lib/bin:$PATH"
setenv PATH "$DIR/cellranger-cs/2.1.1/lib/bin:$PATH"
setenv PATH "$DIR/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c9/bin:$PATH"
setenv PATH "$DIR/cellranger-tiny-ref/1.2.0:$PATH"
setenv PATH "$DIR/cellranger-tiny-fastq/1.2.0:$PATH"
setenv PATH "$DIR/samtools_new/1.6:$PATH"


#
# Module-specific env vars
#
# martian-cs

if ( ! $?PYTHONPATH ) then
    setenv PYTHONPATH "$DIR/martian-cs/2.3.2/adapters/python"
else
    setenv PYTHONPATH "$DIR/martian-cs/2.3.2/adapters/python:$PYTHONPATH"
endif
# cellranger-cs
setenv MROFLAGS "--vdrmode=rolling"
setenv LC_ALL "C"
setenv MROPATH "$DIR/cellranger-cs/2.1.1/mro"

if ( ! $?MROPATH ) then
    setenv MROPATH "$DIR/cellranger-cs/2.1.1/tenkit/mro"
else
    setenv MROPATH "$DIR/cellranger-cs/2.1.1/tenkit/mro:$MROPATH"
endif
setenv PYTHONPATH "$DIR/cellranger-cs/2.1.1/lib/python:$PYTHONPATH"
setenv PYTHONPATH "$DIR/cellranger-cs/2.1.1/tenkit/lib/python:$PYTHONPATH"
setenv PYTHONUSERBASE "$DIR/cellranger-cs/2.1.1/lib"