-
Notifications
You must be signed in to change notification settings - Fork 6
/
call_defuse.sh
36 lines (31 loc) · 683 Bytes
/
call_defuse.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
#!/bin/bash
#
#
. common.sh
CALLER=defuse/0.8.0
DEFUSE_DIR=$BASE_DIR/tools/defuse/0.8.0
DEFUSE_DATADIR=$BASE_DIR/tools/defuse/dataset_directory
export PATH=$DEFUSE_DIR/scripts:$PATH
# Reference preprocessing
# defuse_create_ref.pl -d $DEFUSE_DATADIR -c $DEFUSE_DIR/scripts/config.txt
for FQ1 in $DATA_DIR/*.1.fq ; do
cx_load $FQ1
CX_CALLER=$CALLER
CX_FQ1=$FQ1
CX_FQ2=${FQ1/.1./.2.}
cx_save
XC_OUTPUT=$CX/results.tsv
XC_SCRIPT="
#rm -rf $CX;
mkdir -p $CX 2>/dev/null; cd $CX;
module add samtools bowtie ucsc-tools R gmap-gsnap
defuse_run.pl \
-c $DEFUSE_DIR/scripts/config.txt \
-d $DEFUSE_DATADIR \
-1 $CX_FQ1 \
-2 $CX_FQ2 \
-o $CX \
-p $MAX_CORES
"
xc_exec
done