Hello there
Here is a bash script that generates a new param file each time.
It is very simple, easy to edit and straightforward, enjoy
#!/bin/bash
TMPDIR="/state/partition1/mira_UTT_TMP" #change it on the manifest file
RUNDIR="/home/TheGodFather/thunderstorm/TRN/MIRA/"
NORMDIR="/home/TheGodFather/thunderstorm/TRN/NORM_TRIM/"
# Open a temp dir at local machine
rm -rf $TMPDIR
if [ ! -d "$TMPDIR" ]; then
mkdir $TMPDIR
fi
if [ ! -d "$RUNDIR" ]; then
mkdir $RUNDIR
fi
#go to work directory
cd $RUNDIR
#CREATE THE MANIFEST FILE
echo "
#manifest file for testing mira 4
project = UTT_as_MIRA
job = est,denovo,accurate
#parameters = -SB:bft=caf -GE:not=14 -SK:mmhr=1:pr=70:hss=2
parameters = -GE:not=8:kpmf=5 -SK:mmhr=1:pr=70:hss=2 -CL:ascdc=no
-HS:mnr=yes
parameters = COMMON_SETTINGS -AS:sd=y:nop=2 -DI:trt=$TMPDIR
parameters = SOLEXA_SETTINGS -CL:qc=yes:qcmq=5:qcwl=5 -AS:mrpc=3
# now the shotgun Illumina data
readgroup = DataForShotgunIllumina
data = $TMPDIR\/SE.fastq
technology = solexa
readgroup = DataIlluminaPairedLib
autopairing
data = $TMPDIR\/PE1.fastq $TMPDIR\/PE2.fastq
technology = solexa
" > $RUNDIR/UTT_as_manifest.dat
~/programas/mira4/bin/mira -M UTT_as_manifest.dat
~/programas/mira4/bin/mira UTT_as_manifest.dat
echo "it is over"
