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YAP.rc
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YAP.rc
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#!/bin/bash
## Environment file to be sourced (not runned!!!) by both the entry scripts
## on the submit host and job scripts when executing on the compute nodes
## This uses BASH v.3 specific variables to determine its own location
#################################################################
## You probably only ever will change this if you are a developer
#################################################################
## name of the file that is "sourced" (only BASH v.3!!!)
this_script=${BASH_SOURCE[0]}
this_script_base=$(basename "$this_script")
## abs path to this dir
this_script_dir=$(cd $(dirname "$this_script") && pwd)
export YAP_RC="$this_script_dir/$this_script_base"
export YAP_SCRIPTS="$this_script_dir"
export YAP_WRAPPER="$YAP_SCRIPTS/YAP_wrapper"
#################################################################
## These you might want to change if you moved the dependencies
#################################################################
## Environment variables that YAP code needs to be defined
export YAP_DEPS="/home/atovtchi/work/YAP.deps/bin"
## This will be used if --annotations argument is not passed to entry script
export YAP_DATA="/home/atovtchi/work/YAP.deps/ANNOTATION/"
source /usr/local/sge_current/jcvi/common/settings.sh
export PATH=$YAP_DEPS:/usr/local/packages/graphviz/bin:$PATH
# make sure all the libraries are linked
export LD_LIBRARY_PATH=/usr/local/packages/mysql/lib:/usr/local/packages/gcc/lib64:/usr/local/packages/curl/lib:$LD_LIBRARY_PATH
#################################################################
#################################################################
## Soemwhat mitigate the problem that YAP needs lots of file
## descriptors on large runs:
ulimit -n hard