prehensilecode

#!/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

prehensilecode

@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;
}

prehensilecode

#!/usr/bin/env python3
import sys
import os

print('hello, world')

prehensilecode

#!/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')

prehensilecode

NGS

• Documentation: https://github.com/ncbi/ngs/wiki/Building-and-Installing-from-Source
• This contains:
  • DEPRECATED ngs-bam
  • ngs-java
  • ngs-python (optional)
  • ngs-sdk

Modules:

• gcc/9.2.0

prehensilecode

#!/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()

prehensilecode

#!/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)

prehensilecode

#!/bin/bash
awk '{print $1, "slots=" $2, "maxslots=" $2}' ${PE_HOSTFILE} > myhostfile.${JOB_ID}

prehensilecode

#!/usr/bin/env python3
import sys, os
import csv
import pandas as pd
import argparse

def read_csv(csvfile):
    print('read_csv(): type(csvfile)) = {}'.format(csvfile))
    print('')

prehensilecode