#!/bin/bash -l
# Tisha Melia
# June 23, 2015
#
# Create cufflinks reconstruction for each sample
# All lines starting with "#$" are SGE qsub commands
# It accepts 4 command line arguments with of files to run
# 
# qsub -N name -P waxmanlab -pe single_node 2-8 -l h_rt=72:00:00 cufflinks.qsub [SAMPLE_NAME] [STRANDEDNESS] [BASE_INPUT_FILE] [BASE_OUTPUT_DIR]

# Specify which shell to use
#$ -S /bin/bash
# Run on the current working directory
#$ -cwd

# Join standard output and error to a single file
#$ -j y

# Send an email when the job begins and when it ends running


# Whom to send the email to


#checking the command line arg
if [ $# -lt 4 ] ; then
      echo "Need 4 command line arguments to run"
      echo "qsub -N name -P waxmanlab -pe single_node 2-8 -l h_rt=72:00:00 cufflinks.qsub [SAMPLE_NAME] [STRANDEDNESS] [BASE_INPUT_FILE] [BASE_OUTPUT_DIR]"
      exit 0
fi


#

SAMPLE_NAME=$1
STRANDEDNESS=$2
BASE_INPUT_FILE=$3
BASE_OUTPUT_DIR=$4

BASE_AUX_DIR="/restricted/projectnb/waxmanlab/varsha/cufflinks"


# Now let's keep track of some information just in case anything goes wrong
echo "=========================================================="
echo "Starting on : $(date)"
echo "Running on node : $(hostname)"
echo "Current directory : $(pwd)"
echo "Current job ID : $JOB_ID"
echo "Current job name : $JOB_NAME"
echo "Task index number : $TASK_ID"
echo "=========================================================="


# Go to local scratch directory
cd ${TMPDIR}
ls 
echo $TMPDIR

# print out some diagnostic stuff
echo Running on host `hostname`
echo
echo Directory is `pwd`
echo
echo Start time is `date`
echo


module load boost/1.69.0
module load samtools/0.1.19
module load bowtie2/2.3.4.1
module load cufflinks/2.2.1
module load python3


echo "copying..."
# copy user input date files to scratch


cp $BASE_INPUT_FILE mapped.bam
cp ${BASE_AUX_DIR}/genomeWithRandom.fa . #exactly the same as the previous one
cp ${BASE_AUX_DIR}/genes.gtf .

echo "Current dir:"
pwd

# run my commands
echo
echo "running commands..."
echo
ls *

OUTPUT_DIR="${SAMPLE_NAME}_cufflinks"

cufflinks -o ${OUTPUT_DIR} -p $NSLOTS -g genes.gtf -b genomeWithRandom.fa -u --library-type $STRANDEDNESS mapped.bam
echo "cufflinks -o ${OUTPUT_DIR} -p $NSLOTS -g genes.gtf -b genomeWithRandom.fa -u --library-type $STRANDEDNESS mapped.bam"
#cufflinks -o ${OUTPUT_DIR} -p $NSLOTS -g genes.gtf --library-type $STRANDEDNESS mapped.bam
#echo "cufflinks -o ${OUTPUT_DIR} -p $NSLOTS -g genes.gtf --library-type $STRANDEDNESS mapped.bam"


#Usage:   cufflinks [options] <hits.sam>
#General Options:
#  -o/--output-dir              write all output files to this directory              [ default:     ./ ]
#  -p/--num-threads             number of threads used during analysis                [ default:      1 ]
#  --seed                       value of random number generator seed                 [ default:      0 ]
#  -G/--GTF                     quantitate against reference transcript annotations                      
#  -g/--GTF-guide               use reference transcript annotation to guide assembly                   
#  -M/--mask-file               ignore all alignment within transcripts in this file                     
#  -b/--frag-bias-correct       use bias correction - reference fasta required        [ default:   NULL ]
#  -u/--multi-read-correct      use 'rescue method' for multi-reads (more accurate)   [ default:  FALSE ]
#  --library-type               library prep used for input reads                     [ default:  below ]

# copy the output files to users storage dir
cp -r ${OUTPUT_DIR} ${BASE_OUTPUT_DIR}/.

echo "done running. copying..."
#Just list everything in scratch dir (Don't know what output files I need)
echo "List of files in scratch"
ls * 
#Also want the file size of everything
echo "Size of files in scratch"
du -ch *

# print out some diagnostic stuff
echo Stop time is `date`