GPL16043.sh

#!/usr/bin/bash
# The MIT License (MIT)

# Copyright (c) 2013 Charles Lin

# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.

# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.


#first make temp directory

#get the zip of the cel files and the name of the zip
CEL_ZIP=$1
NAME=$2

#CEL_ZIP=/ark/home/cl512/ressrv19/raw/expression/JB20130926st.zip
#NAME=AFFY
ID=$RANDOM
#ID=1234
TEMP_DIR_ROOT=/ark/temp/
TEMP_DIR=$TEMP_DIR_ROOT$NAME\_tmp\_$ID
INITIAL_DIR=`pwd`

#making the temp directory
mkdir $TEMP_DIR

#copy and unzip stuff
cp $CEL_ZIP $TEMP_DIR/$NAME\_tmp_$ID.zip
cd $TEMP_DIR
unzip $TEMP_DIR/$NAME\_tmp_$ID.zip

#make an analysis output directory
mkdir $TEMP_DIR/output

#run the spikey normy
R --no-save $TEMP_DIR/ $NAME < $INITIAL_DIR/GPL16043.r

#run the GPL gene level script
python $INITIAL_DIR/GPL16043.py -i $TEMP_DIR/output/$NAME\_all_mas5_probe_exprs_raw.txt
python $INITIAL_DIR/GPL16043.py -i $TEMP_DIR/output/$NAME\_all_mas5_probe_exprs_norm.txt

#zip up the output
cd $TEMP_DIR
zip -r $NAME\_output.zip output

echo "WROTE OUTPUT TO: " $TEMP_DIR/$NAME\_output.zip