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monger
executable file
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monger
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#!/usr/bin/env bash
#define MAX_ARG_PAGES 32
set -e
export SHELL=$(type -p bash)
. ~/.bashrc
# freemem=`free | awk '{print $4}'`
# freemem=`echo $freemem | cut -d' ' -f4`
# MEMLIMIT=`expr $freemem \/ 4 \* 3`
# ulimit -v $MEMLIMIT
###############################################
XMODULE_DIR=
MODULE_NAME=`basename "$0" | tr "[a-z]" "[A-Z]"`
function beginswith {
case $2 in
"$1"*) true;;
*) false
esac
}
###############################################
function monger.run {
####################################
########### FUNCTIONS ##############
####################################
function time_elapsed {
end_time=`date +%s`
elapsed_secs=`expr $end_time - $1`
date -u -d @${elapsed_secs} +"%T"
}
function edit_mongerscript {
if [ $4 ]
then
if `grep -q $'\t'"$2" $4`
then
sed -i "s|\t$2.*|\t$2=$3|" $4
else
var_value=`echo $3 | sed 's|\/|\\\/|g'`
sed -i "/^$1:$/{N;s|\[|\[\n\t$2=$var_value|}" $4
fi
fi
}
# export -f edit_mongerscript
function parse_inputs {
if ! test -f "$1"
then
if ! test -d "$1"
then
echo "MONGER RUN ERROR: Could not find input file or directory $1"
exit 1
else
for file in $1/*
do
inputs="$inputs $file"
done
fi
else
inputs=$1
fi
echo $inputs
}
# export -f parse_inputs
function run_element {
run_element=$1
mongerscript=$2
io_direction=$3
outdir=$4
MODULE_DIR=$5
input_file=$6
basename=$7
force=$8
element_opts=$9
# re_memlimit=${10}
if [ "$force" == "true" ]
then
# echo "force=$force"
force="-f"
else
force=""
fi
if `echo $element | grep -q ":"`
then
program=`echo $run_element | cut -d":" -f1`
module_args=`echo $run_element | cut -d":" -f2`
else
program=$run_element
fi
mkdir -p $outdir/input_variables
module=`find $MODULE_DIR -maxdepth 4 -name "$program"`
if [ "$module" == "" ]
then
echo -e "\nMONGER RUN ERROR: Could not find the MongerModule \"$program\" in $MODULE_DIR.\n"
exit -1
fi
input_1=`awk '{print $1}' $input_file | tr "\n" " " | sed 's/\(^\| \)-\($\| \)/ /g'`
input_2=`awk '{print $2}' $input_file | tr "\n" " " | sed 's/\(^\| \)-\($\| \)/ /g'`
input_3=`awk '{print $3}' $input_file | tr "\n" " " | sed 's/\(^\| \)-\($\| \)/ /g'`
names=`awk '{print $4}' $input_file | tr "\n" " " | sed 's/\(^\| \)-\($\| \)/ /g'`
if [ "$io_direction" == "->" ] || [ "$io_direction" == "-|" ]
then
parseMongerScript.pl \
-i $mongerscript \
-a "PROJECT_INFO $element_opts" \
-o $outdir/input_variables/$basename.info.tmp
echo "name=$basename" >> $outdir/input_variables/$basename.info.tmp
if [ "$io_direction" == "-|" ] || [ "$io_direction" == "=|" ]
then
set +e
fi
$module run -I $input_file \
--args $outdir/input_variables/$basename.info.tmp \
-o $outdir \
$force
set -e
else
parseMongerScript.pl \
-i $mongerscript \
-a "PROJECT_INFO $module_args PROGRAM_ARGUMENTS" \
-o $outdir/$basename/info.tmp
module_args=`echo $module_args | sed 's|\s| ::: |g'`
set +e
parallel -j 1 -k $module ::: run \
::: -1 ::: $input_1 \
::: -2 ::: $input_2 \
::: -3 ::: $input_3 \
::: -n ::: $names \
::: -o ::: $outdir/$basename \
::: --args ::: $outdir/$basename/info.tmp \
$module_args ::: $force
set -e
if [ "$io_direction" != "=|" ]
then
for name in $names
do
cat $outdir/$basename/$name/outputs.txt >> $outdir/$basename/outputs.txt
done
fi
fi
}
export -f run_element
function run_mongerscript {
input_file=$1
mongerscript=$2
# rm_memlimit=$3
# Get relevant variables from mongerscript
rm -rf /tmp/mongerinfo.tmp
parseMongerScript.pl \
-i $mongerscript \
-a "PROJECT_INFO INPUT_INFO PROGRAM PROGRAM_ELEMENTS MODULE_ARGUMENTS" \
-o /tmp/mongerinfo.tmp
. /tmp/mongerinfo.tmp
mkdir -p $OUTPUT_DIRECTORY/$PROJECT_NAME/logs
mkdir -p $OUTPUT_DIRECTORY/$PROJECT_NAME/program_logs
mkdir -p $OUTPUT_DIRECTORY/$PROJECT_NAME/commands
field_num=`awk -F'[\t ]' '{print NF}' $input_file`
basename=`awk -F'[\t ]' -v last_field="$field_num" '{print $last_field}' $input_file | head -1`
lasting_basename=$basename
main_start=`date +%s`
time=`date +%y%m%e_%H%M%S`
echo -e "##############\n\
MAIN_$time:" >> $OUTPUT_DIRECTORY/$PROJECT_NAME/logs/$basename.log.txt
echo -e "##############\n\
MAIN_$time:" >> $OUTPUT_DIRECTORY/$PROJECT_NAME/program_logs/$basename.program_log.txt
echo -e "##############\n\
# MAIN_$time:" >> $OUTPUT_DIRECTORY/$PROJECT_NAME/commands/$basename.commands.txt
# Set input option to be all files separately
element_io="->"
element_input=$input_file
for element in $RUN_PROGRAM
do
first_subelement=true
if [ "$element" != "->" ] && [ "$element" != "=>" ] &&\
[ "$element" != "-|" ] && [ "$element" != "=|" ]
then
# Record element start time
element_caps=`echo $element | tr '[a-z]' '[A-Z]'`
element_start=`date +%s`
echo -e "\t$element_caps:" >> $OUTPUT_DIRECTORY/$PROJECT_NAME/logs/$basename.log.txt
echo -e "$element_caps:" >> $OUTPUT_DIRECTORY/$PROJECT_NAME/program_logs/$basename.program_log.txt
echo -e "# $element_caps" >> $OUTPUT_DIRECTORY/$PROJECT_NAME/commands/$basename.commands.txt
#
element_name=$element
# Get components (subelements) of current program element
element=${!element_name}
# Assign subelement input and input options to default settings if first process
if [ "$first_subelement" == "true" ]
then
subelement_input=$element_input
subelement_io=$element_io
fi
# If no subelements of current element, try to run as independent thing.
if [ "$element" == "" ]
then
element=$element_name
fi
# Execute each subelement
for subelement in $element
do
if [ "$subelement" != "->" ] && [ "$subelement" != "=>" ] &&\
[ "$subelement" != "-|" ] && [ "$subelement" != "=|" ] &&\
[ "$subelement" != "+" ]
then
# Determine if subelement is beginning of a groupped set of subelements (subprocess i.e. Should be run in parallel)
if `echo $subelement | grep -q "^("` && [ "$PARALLEL" == "TRUE" ]
then
subprocess_subelements=${subelement:1}
subprocess=true
# If subelement is not a component of a subprocess run normally
elif [ "$subprocess" != "true" ] || [ "$PARALLEL" != "TRUE" ]
then
if `echo $subelement | grep -q "^("`
then
subelement_name=${subelement:1}
subprocess=start
elif `echo $subelement | grep -q ")$"`
then
subelement_name=${subelement:0:${#subelement}-1}
subprocess=end
else
# Record subelement start time
subelement_name=`echo $subelement | awk -F':' '{print $1}'`
fi
subelement_opts=`echo $subelement | awk -F':' '{print $2}'`
if [ "$element_name" == "$subelement" ]
then
subelement_outdir=$OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name
else
if [ `echo "$element" | sed "s| |\n|g" | grep -c "$subelement"` -gt 1 ]
then
var="number_$subelement"
new_num=$((${!var} + 1 ))
declare "number_$subelement=$new_num"
if [ "$subelement_opts" != "" ]
then
subelement_outdir=$OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$subelement_name.$subelement_opts.${!var}
else
subelement_outdir=$OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$subelement_name.${!var}
fi
else
if [ "$subelement_opts" != "" ]
then
subelement_outdir=$OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$subelement_name.$subelement_opts
else
subelement_outdir=$OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$subelement_name
fi
fi
fi
field_num=`awk -F'[\t ]' '{print NF}' $subelement_input`
basename=`awk -F'[\t ]' -v last_field="$field_num" '{print $last_field}' $subelement_input | head -1`
if [ "$subelement_io" == "=>" ] || [ "$subelement_io" == "=|" ]
then
basename=${basename%.*}
fi
if [ "$subelement_io" == "+" ] || [ "$subprocess" != "" ]
then
basename="$basename.$subelement_name"
fi
force=false
for f in $FORCE
do
case "$f" in
"$subelement_name" | "$element_name")
force=true;;
esac
done
run_element \
$subelement_name \
$mongerscript \
$subelement_io \
$subelement_outdir \
$MODULE_DIR \
$subelement_input \
$basename \
$force \
$subelement_opts
if test -f $subelement_outdir/outputs/$basename.outputs.txt
then
if [ "$subelement_io" != "-|" ] && [ "$subelement_io" != "=|" ] && [ "$subelement_io" != "+" ] && [ "$subprocess" == "" ]
then
subelement_input=$subelement_outdir/outputs/$basename.outputs.txt
elif [ "$subelement_io" == "+" ] || [ "$subprocess" != "" ]
then
newfield_num=`head -1 $subelement_outdir/outputs/$basename.outputs.txt | awk -F'[\t ]' '{print NF}'`
new=`head -1 $subelement_outdir/outputs/$basename.outputs.txt | awk -F'[\t ]' -v last_field="$newfield_num" '{$last_field = ""; print}'`
if [ "$subsubelement_out" == "" ]
then
subsubelement_out="$new"
else
subsubelement_out="$subsubelement_out $new"
fi
echo "$subsubelement_out $lasting_basename.$element_name" | tr ' ' '\t' > $OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$lasting_basename.current_outputs
if [ "$subprocess" == "end" ]
then
subelement_input=$OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$lasting_basename.current_outputs
subprocess=""
fi
fi
fi
sed 's/^/\t\t/' $subelement_outdir/logs/$basename.log.txt >> $OUTPUT_DIRECTORY/$PROJECT_NAME/logs/$basename.log.txt
cat $subelement_outdir/program_logs/$basename.program_log.txt >> $OUTPUT_DIRECTORY/$PROJECT_NAME/program_logs/$basename.program_log.txt
cat $subelement_outdir/commands/$basename.commands.txt >> $OUTPUT_DIRECTORY/$PROJECT_NAME/commands/$basename.commands.txt
elif `echo $subelement | grep -q ")$"` && [ "$PARALLEL" == "true" ]
then
last_subprocess_subelement=${subelement:0:${#subelement}-1}
subprocess_subelements="$subprocess_subelements $last_subprocess_subelement"
subelement_outdirs=`parallel echo \
::: $OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/ \
::: $subprocess_subelements | \
tr -d " "`
basename=`cut -d" " -f4 $subelement_input | tr "\n" " " | head -1`
if [ "$subelement_io" == "=>" ] || [ "$subelement_io" == "=|" ]
then
basename=${basename%.*}
fi
for subprocess_subelement in $subprocess_subelements
do
if `echo "$FORCE" | grep -q "$subprocess_subelement"` || `echo "$FORCE" | grep -q "$element_name"`
then
force="$force true"
else
force="$force false"
fi
module_arg=$subelement"_modargs"
module_arg=${!module_arg}
if [ "$module_arg" != "" ]
then
module_args="$module_args \"$module_arg\""
else
module_args="$module_args \"0\""
fi
done
# echo -e "$first_args"
# echo -e \
# "parallel --link run_element\n\
# ::: $subprocess_subelements\n\
# ::: $mongerscript\n\
# ::: $subelement_io\n\
# ::: $subelement_outdirs\n\
# ::: $MODULE_DIR\n\
# ::: $subelement_input\n\
# ::: $basename\n\
# ::: $force\n\
# ::: $module_args"
# subpro_count=`echo $subprocess_subelements | wc -w`
# subjobnum=`expr $SUBTHREADS \/ $subpro_count`
# if [ $subjobnum -lt 1 ]
# then
# subjobnum=1
# elif [ $subjobnum -ge 1 ]
# then
# subjobnum=$subpro_count
# fi
# re_memlimit=`expr $rm_memlimit \/ $subjobnum`
# echo "$run_element_memlimit"
parallel -j 1 --link run_element ::: $subprocess_subelements \
::: $mongerscript \
::: $subelement_io \
::: $subelement_outdirs \
::: $MODULE_DIR \
::: $subelement_input \
::: $basename \
::: $force \
::: $module_args
if [ "$subelement_io" != "-|" ] && [ "$subelement_io" != "=|" ]
then
rm -rf $OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$basename.outputs.txt
for sub_outdir in $subelement_outdirs
do
if test -f "$sub_outdir/$basename/output.txt"
then
cat $sub_outdir/$basename/output.txt >> $OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/$basename.outputs.txt
fi
if test -f "$sub_outdir/$basename/log.txt"
then
cat $sub_outdir/$basename/log.txt >> $OUTPUT_DIRECTORY/$PROJECT_NAME/logs/$basename.log.txt
fi
done
fi
subprocess=false
else
subprocess_subelements="$subprocess_subelements $subelement"
fi
elif [ "$subprocess" == "" ]
then
subelement_io=$subelement
else
subsubelement_io=$subelement
fi
first_subelement=false
done
if [ "$element_io" != "-|" ] || [ "$element_io" != "=|" ]
then
element_input=$subelement_input
fi
# Record element time duration
element_elapsed=`time_elapsed $element_start`
sed -i "s|$element_caps\:.*|$element_caps\: $element_elapsed|" $OUTPUT_DIRECTORY/$PROJECT_NAME/logs/$basename.log.txt
################
mkdir -p $OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/element_outputs
field_num=`awk '{print NF}' $subelement_input`
name=`awk -v last_field="$field_num" '{print $last_field}' $subelement_input`
index=1
while [ $index -lt $field_num ]
do
outfile=`awk -v field="$index" '{print $field}' $subelement_input`
cp $outfile $OUTPUT_DIRECTORY/$PROJECT_NAME/$element_name/element_outputs/
index=$(($index + 1))
done
else
element_io=$element
fi
done
# Record element time duration
main_elapsed=`time_elapsed $main_start`
sed -i "s|MAIN_$time\:.*|MAIN_$time\: $main_elapsed|" $OUTPUT_DIRECTORY/$PROJECT_NAME/logs/$basename.log.txt
}
export -f run_mongerscript
####################################
############ USAGE #################
####################################
OUTPUT_DIRECTORY=~/monger.output
PROJECT_NAME=`date +"%d-%m-%y"`
PHRED_BASE=33
THREADS=1 #`nproc`
SUBTHREADS=1
SEQUENCING_FORMAT=se
XMODULE_DIR=
PAIRED=1
help=false
usage=\
"\nSYNOPSIS:\n\
monger run <PROGRAM/MONGERSCRIPT>\n\n\
DESCRIPTION:\n\
Runs an NGS program (as a MongerModule) or MongerScript through Monger.\n\n\
OPTIONS:\n\
-M | --MODULE_DIR\t[DIR]\tDirectory in which to search for MongerModules[$MODULE_DIR].\n\
-T | --THREADS\t[INT]\tTotal number of threads to allocate [$THREADS]\n\
-t | --SUBTHREADS\t[INT]\tNumber of threads to make available to each input being processed [1]\n\
-a | --args\t[STR]\tQuoted string containing arguments for the specified MongerModule (if not a MongerScript). To access a MongerModule's usage type 'monger run <PROGRAM> -h .\n\n\
Project Info:\n\
-o | --OUTPUT_DIRECTORY\t[DIR]\tOutput directory [~/monger.output]\n\
-p | --PROJECT_NAME\t[STR]\tName of project. This helps differentiate different runs [DATE]\n\
-b | --PHRED_BASE\t[33|64]\tFor FASTQ inputs, phred quality base score.[33]\n\
-f | --SEQUENCING_FORMAT\t[se|pe|mp]\tFormat of FASTA/FASTQ files (se=Single-end, pe=Paired-end, mp=Mate-Pair)[se]\n\
-P | --PLOIDY\t[haploid|diploid]\n\
-Rf | --REFERENCE_FASTA\t[FILE]\n\
-Rg | --REFERENCE_GFF\t[FILE]\tGFF3 formated reference annotations.\n\
-F | --FORCE\t[STR]\tForce rerun element or module (ALL=Force rerun all elements).\n\n\
Input Info:\n\
-i | --INPUTS\t[FILE/DIR]\tInput file(s) or directory containing input files.\n\
-I | --INPUTS_LIST\t[FILE]\tText file containing files to input. Files should be one per line for single-end, two for mates.\n\
-x | --PAIRED [INT]\tIf input files are paired and but not specified in a list, the field relative to end (based on \"_\" as separator) in each name that indicates pair number\n\n\
Program:\n\
-r | --RUN_PROGRAM\t[STR]\tString representing how inputs should be processed (for more details see manual)\n\n\
-h | --help\t\t\tPrint help message\n\n\
AUTHOR:\n\
Noah Gettle 2016"
####################################
######## INPUT PROCESSING ##########
####################################
# Read in inputs #
if [ $# -eq 0 ]
then
echo -e $usage
exit 1
fi
input_num=$#
if `beginswith "-" $1`
then
if [ "$1" == "-h" ] || [ "$1" == "--help" ]
then
echo -e $usage
exit 1
fi
else
if test -f "$1"
then
if [ `head -1 $1` == "#mongerscript" ]
then
MONGERSCRIPT=$1
shift
cp $MONGERSCRIPT /tmp/mongerscript.txt
MONGERSCRIPT=/tmp/mongerscript.txt
if ! test -f $MONGERSCRIPT
then
echo -e "\nMONGER RUN ERROR: Could not find MongerScript $MONGERSCRIPT.\n"
exit -1
else
# Add default info to script
DEFAULTS="OUTPUT_DIRECTORY PROJECT_NAME PHRED_BASE THREADS SUBTHREADS SEQUENCING_FORMAT MODULE_DIR"
for default in $DEFAULTS
do
if ! `grep -q $'\t'"$default" $MONGERSCRIPT` || `grep -q $'\t'"$default=$" $MONGERSCRIPT` || `grep -q $'\t'"$default$" $MONGERSCRIPT`
then
edit_mongerscript PROJECT_INFO $default ${!default} $MONGERSCRIPT
fi
done
if ! `grep -q $'\tPAIRED' $MONGERSCRIPT` || `grep -q $'\tPAIRED=$' $MONGERSCRIPT` || `grep -q $'\tPAIRED$' $MONGERSCRIPT`
then
edit_mongerscript INPUT_INFO PAIRED $PAIRED $MONGERSCRIPT
fi
parseMongerScript.pl \
-i $MONGERSCRIPT \
-a "PROJECT_INFO INPUT_INFO PROGRAM PROGRAM_ELEMENTS" \
-o /tmp/mongerinfo.tmp
. /tmp/mongerinfo.tmp
# rm -rf /tmp/mongerinfo.tmp
fi
if ! test -d $MODULE_DIR
then
echo -e "\nMONGER RUN ERROR: MongerModule directory $MONGER_DIR does not exist.\n"
exit 1
fi
else
program=$1
shift
fi
else
program=$1
shift
fi
fi
while [ "$1" != "" ]
do
case $1 in
-M | MODULE_DIR)
if ! `beginswith "-" $2`
then
shift
MODULE_DIR=$1
edit_mongerscript PROJECT_INFO MODULE_DIR $1 $MONGERSCRIPT
fi;;
-T | THREADS)
if ! `beginswith "-" $2`
then
shift
THREADS=$1
edit_mongerscript PROJECT_INFO THREADS $1 $MONGERSCRIPT
fi;;
-t | SUBTHREADS)
if ! `beginswith "-" $2`
then
shift
SUBTHREADS=$1
edit_mongerscript PROJECT_INFO SUBTHREADS $1 $MONGERSCRIPT
fi;;
-a | --args)
shift
args=$1;;
-o | --OUTPUT_DIRECTORY)
if ! `beginswith "-" "$2"`
then
shift
OUTPUT_DIRECTORY=$1
edit_mongerscript PROJECT_INFO OUTPUT_DIRECTORY $1 $MONGERSCRIPT
fi;;
-p | --PROJECT_NAME)
shift
PROJECT_NAME=$1
edit_mongerscript PROJECT_INFO PROJECT_NAME $1 $MONGERSCRIPT;;
-b | --PHRED_BASE)
if ! `beginswith "-" $2`
then
shift
PHRED_BASE=$1
if [ "$PHRED_BASE" != "33" ] && [ "$PHRED_BASE" != "64" ]
then
echo -e "MONGER RUN WARNING: The phred-base argument (-b | --PHRED_BASE) you specified ($PHRED_BASE) is not valid (33|64). Treating as \"33\"..."
PHRED_BASE=33
fi
edit_mongerscript PROJECT_INFO PHRED_BASE $1 $MONGERSCRIPT
fi;;
-f | --SEQUENCING_FORMAT)
if ! `beginswith "-" $2`
then
shift
SEQUENCING_FORMAT="`echo $1 | tr "[A-Z]" "[a-z]"`"
if [ "$SEQUENCING_FORMAT" != "se" ] && [ "$SEQUENCING_FORMAT" != "pe" ] && [ "$SEQUENCING_FORMAT" != "mp" ]
then
echo -e "MONGER RUN WARNING: The sequencing format argument (-f | --SEQUENCING_FORMAT) you specified ($SEQUENCING_FORMAT) is not valid (se|pe|mp). Treating as \"se\"..."
SEQUENCING_FORMAT="se"
fi
edit_mongerscript PROJECT_INFO SEQUENCING_FORMAT $1 $MONGERSCRIPT
fi;;
-P | --PLOIDY)
if ! `beginswith "-" "$2"`
then
shift
PLOIDY=$1
edit_mongerscript PROJECT_INFO PLOIDY $1 $MONGERSCRIPT
fi;;
-Rf | --REFERENCE_FASTA)
if ! `beginswith "-" "$2"`
then
shift
REFERENCE_FASTA=$1
edit_mongerscript PROJECT_INFO REFERENCE_FASTA $1 $MONGERSCRIPT
fi;;
-Rg | --REFERENCE_GFF)
if ! `beginswith "-" "$2"`
then
shift
REFERENCE_GFF=$1
edit_mongerscript PROJECT_INFO REFERENCE_GFF $1 $MONGERSCRIPT
fi;;
-F | --FORCE)
while ! `beginswith "-" "$2"` && [ "$2" != "" ]
do
shift
FORCE="$FORCE $1"
done
edit_mongerscript PROJECT_INFOFORCE "$1" $MONGERSCRIPT;;
-i | --INPUTS)
while ! `beginswith "-" "$2"` && [ "$2" != "" ]
do
shift
INPUTS="$INPUTS $1"
done
edit_mongerscript INPUT_INFO INPUTS "$1" $MONGERSCRIPT;;
-I | --INPUTS_LIST)
while ! `beginswith "-" "$2"` && [ "$2" != "" ]
do
shift
INPUTS_LIST="$INPUTS_LIST $1"
done
edit_mongerscript INPUT_INFO INPUTS_LIST "$1" $MONGERSCRIPT;;
-x | --PAIRED)
if ! `beginswith "-" "$2"`
then
shift
PAIRED=$1
edit_mongerscript INPUT_INFO PAIRED "$1" $MONGERSCRIPT
fi;;
-r | --RUN_PROGRAM)
if ! `beginswith "-" "$2"`
then
shift
RUN_PROGRAM=$1
edit_mongerscript PROGRAM RUN_PROGRAM "$1" $MONGERSCRIPT
fi;;
-h | --help)
help=true;;
*)
echo -e "MONGER RUN ERROR: \"$1\" not recognized as a valid option."
exit 1;;
esac
shift
done
# Check inputs #
if [ "$MONGERSCRIPT" == "" ]
then
if [ "$program" != "" ]
then
if ! test -d $MODULE_DIR
then
echo -e "\nMONGER RUN ERROR: MongerModule directory $MODULE_DIR does not exist.\n"
exit 1
fi
if `echo $program | grep -qv "./."`
then
module=`find $MODULE_DIR -maxdepth 4 -name "$program"`
fi
if [ "$module" == "" ]
then
echo -e "\nMONGER RUN ERROR: Could not find the MongerModule \"$program\" in $MODULE_DIR. If this is a MongerScript, it needs to start with \"#mongerscript\".\n"
exit 1
else
input_helptest="$INPUTS $INPUTS_LIST"
if [ "$help" == "true" ] || [ "$input_helptest" == " " ]
then
$module run -h
fi
RUN_PROGRAM=$program
fi
fi
fi
MAIN_DIR=$OUTPUT_DIRECTORY/$PROJECT_NAME
mkdir -p $MAIN_DIR
if ! test -d "$MAIN_DIR"
then
echo -e "MONGER RUN ERROR: Could not find or create output directory $MAIN_DIR."
exit 1
fi
rm -rf $MAIN_DIR/input_files.txt
if [ "$INPUTS" != "" ]
then
for input in $INPUTS
do
new_inputs=`parse_inputs $input`
inputs="$inputs $new_inputs"
done
if [ "`echo $SEQUENCING_FORMAT | tr "[A-Z]" "[a-z]"`" == "pe" ] || [ "`echo $SEQUENCING_FORMAT | tr "[A-Z]" "[a-z]"`" == "mp" ]
then
findpairs.pl -p $PAIRED -o $MAIN_DIR/input_files.txt -i "$inputs"
else
for input in $inputs
do
filename=$(basename "$input")
name="${filename%.*}"
echo -e "$input\t$name" >> $MAIN_DIR/input_files.txt
done
fi
fi
if [ "$INPUTS_LIST" != "" ]
then
for list in $INPUTS_LIST
do
if ! test -f "$list"
then
echo -e "MONGER RUN ERROR: Could not find input list file $1"
exit 1
else
cat $list >> $MAIN_DIR/input_files.txt
fi
done
fi
if [ `wc -w $MAIN_DIR/input_files.txt | cut -d" " -f1` -eq 0 ]
then
echo -e "MONGER RUN ERROR: No input files detected."
exit 1
fi
if [ "$RUN_PROGRAM" == "" ]
then
echo -e "\nMONGER RUN ERROR: Could not figure out what to do with the inputs.\n"
exit 1
fi
mkdir -p $MAIN_DIR/mongerscripts
index=1
while test -f "$MAIN_DIR/mongerscripts/mongerscript.$index.txt"
do
index=`expr $index + 1`
done
if [ "$MONGERSCRIPT" == "" ]
then
MONGERSCRIPT=$MAIN_DIR/mongerscripts/mongerscript.$index.txt
echo -e \
"PROJECT_INFO:\n\
[\n\
\tOUTPUT_DIRECTORY=$OUTPUT_DIRECTORY\n\
\tPROJECT_NAME=$PROJECT_NAME\n\
\tPHRED_BASE=$PHRED_BASE\n\
\tSEQUENCING_PLATFORM=$SEQUENCING_PLATFORM\n\
\tTHREADS=$THREADS\n\
\tSEQUENCING_FORMAT=$SEQUENCING_FORMAT\n\
\tPLOIDY=$PLOIDY\n\
\tREFERENCE_FASTA=$REFERENCE_FASTA\n\
\tREFERENCE_GFF=$REFERENCE_GFF\n\
\tMODULE_DIR=$MODULE_DIR\n\
\tFORCE=$FORCE\n\
]\n\
INPUT_INFO:\n\
[\n\
\tINPUTS_LIST=$MAIN_DIR/input_files.txt\n\
]\n\
PROGRAM:\n\
[\n\
\tRUN_PROGRAM=\"$RUN_PROGRAM\"\n\
]\n\
PROGRAM_ELEMENTS:\n\
[\n\
]\n\
MODULE_ARGS:\n\
[
\t$RUN_PROGRAM-modargs=$args\n\
]"\
> $MONGERSCRIPT
else
cp $MONGERSCRIPT $MAIN_DIR/mongerscripts/mongerscript.$index.txt
MONGERSCRIPT=$MAIN_DIR/mongerscripts/mongerscript.$index.txt
fi
####################################
######### RUN MONGERSCRIPT ########
####################################
# while read input_line
# do
# echo $input_line > $MAIN_DIR/current_input.txt
# run_mongerscript $MAIN_DIR/current_input.txt $MONGERSCRIPT
# done < $MAIN_DIR/input_files.txt
mkdir -p $MAIN_DIR/inputs
while read input_line
do
field_num=`echo $input_line | awk -F'[\t ]' '{print NF}'`
name=`echo $input_line | awk -F'[\t ]' -v last_field="$field_num" '{print $last_field}'`
echo "$input_line" > $MAIN_DIR/inputs/$name.inputs.txt
input_files="$input_files $MAIN_DIR/inputs/$name.inputs.txt"
done < $MAIN_DIR/input_files.txt
# jobnum=`expr $THREADS \/ $SUBTHREADS`
# inputnum=`echo $inputs | wc -w`
# if [ $jobnum -eq 0 ]
# then
# jobnum=1
# elif [ $jobnum -gt $inputnum ]
# then
# jobnum=$inputnum
# fi
# echo -e "parallel -j $jobnum -k run_mongerscript \n::: $input_files \n::: $MONGERSCRIPT"
# rm_memlim=`expr $MEMLIMIT \/ $jobnum`
for file in $input_files
do
run_mongerscript $file $MONGERSCRIPT
done
# parallel -j 1 -k run_mongerscript ::: $input_files ::: $MONGERSCRIPT
}
function monger.install {
XINSTALL_DIR=
XMODULE_DIR=
####################################
############ USAGE #################
####################################
usage=\
"SYNOPSIS:\n\
monger install <PROGRAM> [ARGS]\n\n\
DESCRIPTION:\n\
Install programs that are components of Monger pipelines.\
By default, Monger install modules will attempt to determine \
if specified program and its requisite dependencies are already installed. \
If not, an attempt will be made to install these.\n\n\
OPTIONS:\n\
-i | --install_dir\t[DIR]\tInstallation directory [$INSTALL_DIR]\n\
-d | --module_dir\t[DIR]\tDirectory containing Monger install modules [$MODULE_DIR]\n\
-c | --configs\t[FILE]\tConfiguration file\n\
-f | --force\t\t\tOverwrite existing program executables.\n\
-h | --help\t\t\tPrint help message\n\n\
AUTHOR:\n\
Noah Gettle 2016"
####################################
######## INPUT PROCESSING ##########
####################################
if [ $# -eq 0 ]
then
echo -e $usage
exit 1
fi
while ! `beginswith "-" "$1"` && [ "$1" != "" ]
do
if [ "$programs" == "" ]
then
programs=$1
else
programs="$programs $1"
fi
shift
done
while [ "$1" != "" ]
do
case $1 in
-i | --install_dir)
if ! `beginswith "-" "$2"`
then
shift
INSTALL_DIR=$1
fi;;
-d | --module_dir)
if ! `beginswith "-" "$2"`
then
shift
MODULE_DIR=$1
fi;;
-c | --configs)
if ! `beginswith "-" "$2"`
then
shift
. $1
fi;;
-f | --force)
FORCE="-f";;
-h | --help)
if [ "$programs" != "" ]
then
for program in $programs
do
module=`find $MODULE_DIR -maxdepth 4 -name "$program"`
if [ "$module" != "" ]
then
$module install -h
fi
done
else
echo -e $usage
exit 1
fi;;
*)
echo -e "MONGER INSTALL ERROR: \"$1\" not recognized as a valid option\n\n$usage"
exit 1;;
esac
shift
done
####################################
# NEED to change to make more portable #
if ! `echo $PATH | grep -q "$INSTALL_DIR/bin"` # [[ ":$PATH:" != *":$INSTALL_DIR/bin:"* ]]
then
echo "1.5"
if ! `grep -q "^export PATH=" ~/.bashrc` # > /dev/null
then
echo "1.75"
echo -e "export PATH=$INSTALL_DIR/bin:$PATH" >> ~/.bashrc
else
sed -i'' -e "s|export PATH=.*|export PATH=$INSTALL_DIR/bin:$PATH|g" ~/.bashrc
rm -rf ~/.bashrc-e
fi
. ~/.bashrc
fi
if ! `echo $LD_LIBRARY_PATH | grep -q "$INSTALL_DIR/lib"` #[[ ":$LD_LIBRARY_PATH:" != *":$INSTALL_DIR/lib:"* ]]
then
if ! grep "^export LD_LIBRARY_PATH=" ~/.bashrc > /dev/null
then
echo -e "export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH" >> ~/.bashrc
else
sed -i'' -e "s|export LD_LIBRARY_PATH=.*|export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH|g" ~/.bashrc
rm -rf ~/.bashrc-e
fi
. ~/.bashrc
fi
if ! `echo $LD_LIBRARY_PATH | grep -q "$INSTALL_DIR/lib64"` #[[ ":$LD_LIBRARY_PATH:" != *":$INSTALL_DIR/lib64:"* ]]
then
if ! grep "^export LD_LIBRARY_PATH=" ~/.bashrc > /dev/null
then
echo -e "export LD_LIBRARY_PATH=$INSTALL_DIR/lib64:$LD_LIBRARY_PATH" >> ~/.bashrc
else
sed -i'' -e "s|export LD_LIBRARY_PATH=.*|export LD_LIBRARY_PATH=$INSTALL_DIR/lib64:$LD_LIBRARY_PATH|g" ~/.bashrc
rm -rf ~/.bashrc-e
fi
. ~/.bashrc
fi
if ! `echo $INCLUDE | grep -q "$INSTALL_DIR/include"` #[[ ":$INCLUDE:" != *":$INSTALL_DIR/include:"* ]]
then
if ! grep "^export INCLUDE=" ~/.bashrc > /dev/null
then
echo -e "export INCLUDE=$INSTALL_DIR/include:$INCLUDE" >> ~/.bashrc
else
sed -i'' -e "s|export INCLUDE=.*|export INCLUDE=$INSTALL_DIR/include:$INCLUDE|g" ~/.bashrc
rm -rf ~/.bashrc-e
fi
. ~/.bashrc
fi
mkdir -p $INSTALL_DIR/bin
mkdir -p $INSTALL_DIR/include
mkdir -p $INSTALL_DIR/lib
mkdir -p $INSTALL_DIR/lib64
mkdir -p $INSTALL_DIR/etc
mkdir -p $INSTALL_DIR/man
####################################
######## INSTALL MODULES ###########
####################################
for program in $programs
do
if [ "$program" != "" ]
then
module=`find $MODULE_DIR -maxdepth 4 -name "$program"`
if [ "$module" != "" ]
then
$module install -i $INSTALL_DIR $FORCE
else
echo -e "MONGER INSTALL WARNING: Could not find module $program. Skipping..."
fi
fi
done
}
####################################
############ USAGE #################
####################################
usage=\
"\nSYNOPSIS:\n\
monger <run|install> <MODULE>\n\n\
DESCRIPTION:\n\
MOdular Next-Gen sequence processing and analysis program.\n\n\
To see function specific arguments type \"monger <run|install> --help\".\n
To see module specific arguments type \"monger <run|install> <MODULE> --help\".\n\n\