- Documentation: https://github.com/ncbi/ngs/wiki/Building-and-Installing-from-Source
- This contains:
- DEPRECATED
ngs-bam - ngs-java
- ngs-python (optional)
- ngs-sdk
- DEPRECATED
Modules:
- gcc/9.2.0
python-lsp-server | |
importmagic | |
epc | |
pycodestyle | |
mccabe | |
pyflakes | |
pylint | |
rope | |
yapf | |
ipython |
#!/usr/bin/env python | |
import sys | |
import os | |
import numpy as np | |
text = [[4, 3, 8, 9, 5, 1, 2, 7, 6], [8, 3, 4, 1, 5, 9, 6, 7, 2], | |
[6, 1, 8, 7, 5, 3, 2, 9, 4], [6, 9, 8, 7, 5, 3, 2, 1, 4], | |
[6, 1, 8, 7, 5, 3, 2, 1, 4], [6, 1, 3, 2, 9, 4, 8, 7, 5]] | |
text = np.array(text) |
#!/bin/bash | |
module use /ifs/opt/modulefiles | |
module load python/gcc/3.9.1 | |
module load ncbi-blast | |
### About the db sources: | |
### - ncbi provides .tar.gz files, which need to be extracted | |
### - gcp and aws provide all the db files directly | |
logfile=/var/log/blast.log |
@font-face { | |
font-family: 'Meslo LG'; | |
src: url('https://github.com/powerline/fonts/raw/master/Meslo%20Slashed/Meslo%20LG%20M%20Regular%20for%20Powerline.ttf') format('truetype'); | |
font-weight: normal; | |
font-style: normal; | |
} |
#!/usr/bin/env python3 | |
import sys | |
import os | |
print('hello, world') |
#!/usr/bin/env python3 | |
import sys | |
import os | |
import csv | |
import argparse | |
import pathlib | |
parser = argparse.ArgumentParser() | |
parser.add_argument('-d', '--debug', action='store_true', help='Debug') | |
parser.add_argument('-i', '--infile', type=argparse.FileType('r'), help='CSV file from LISTSERV') |
Modules:
#!/usr/bin/env python3 | |
import sys | |
import os | |
from pythoncm.cluster import Cluster | |
from pythoncm.settings import Settings | |
from pythoncm.entity import * | |
debug_p = False | |
cluster = Cluster() |
#!/usr/bin/env python3.6 | |
import numpy as np | |
import tensorflow as tf | |
# Mash-up of: | |
# - https://stackoverflow.com/a/49497004 | |
# - https://ml-with-tensorflow.info/2017/03/01/svm-with-tensorflow/ | |
X = np.zeros([157, 128]) | |
Y = np.zeros([157], dtype=np.int32) |
#!/bin/bash | |
awk '{print $1, "slots=" $2, "maxslots=" $2}' ${PE_HOSTFILE} > myhostfile.${JOB_ID} |