-
Notifications
You must be signed in to change notification settings - Fork 0
/
conifer_make_files.sh
executable file
·49 lines (35 loc) · 1.14 KB
/
conifer_make_files.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
36
37
38
39
40
41
42
43
44
45
46
47
48
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
module load modules modules-init modules-gs
module load zlib/1.2.5
module load hdf5/1.8.8
module load bedtools/latest
module load python/2.7.2
module load lzo/2.06
module load pytables/2.3.1_hdf5-1.8.8
source config.sh
BASE_DIR=$PROJECT_DIR'/SVD_'$SVD_DISCARD
mkdir -p $BASE_DIR
PROBES=$DEFAULT_PROBEFILE
LOGLEVEL="DEBUG"
#CHR=22
TMPDIR=/var/tmp/`whoami`
mkdir -p $TMPDIR
SCRIPT=$CONIFER_SCRIPT_DIR/02_create_conifer_file.py
# setup multithreaded numpy
export PYTHONPATH=/net/eichler/vol8/home/nkrumm/lib/python2.7/site-packages/:$PYTHONPATH
export LD_LIBRARY_PATH=/net/eichler/vol8/home/nkrumm/lib/lib/:$LD_LIBRARY_PATH
export OPENBLAS_NUM_THREADS=6
export OMP_NUM_THREADS=6
# turn off warnings
export PYTHONWARNINGS="ignore"
CONIFER_ANALYSIS_FILE="$BASE_DIR/chr${CHR}.SVD${SVD_DISCARD}.hdf5"
QC_REPORT="$BASE_DIR/chr${CHR}.SVD${SVD_DISCARD}.txt"
python $SCRIPT --outfile $CONIFER_ANALYSIS_FILE \
--components_removed $SVD_DISCARD \
--chromosomes $CHR \
--probes $PROBES \
--samples $SVD_SAMPLE_LIST \
--loglevel $LOGLEVEL \
--QC_report=$QC_REPORT