David Chin prehensilecode

## update_unpack_blastdbs.sh
#!/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

## crosh-font.css
@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;
}

## something.py
#!/usr/bin/env python3
import sys
import os

print('hello, world')

## munge_listserv_subcriber_report.py
#!/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')

## ncbi_ngs_build_rhel8.md

      
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                prehensilecode
                / ncbi_ngs_build_rhel8.md
            
            
              Last active
              November 2, 2023 00:35
            
              
                HOWTO Build NCBI NGS on RHEL 8
              
          
    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


## change_categories_cm9.py
#!/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()

## simple_svm.py
#!/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)

## ge2openmpi.sh
#!/bin/bash
awk '{print $1, "slots=" $2, "maxslots=" $2}' ${PE_HOSTFILE} > myhostfile.${JOB_ID}

## pdreadcsv.py
#!/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('')

## foo.csv

          
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	#!/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 python3.6
	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}
	#!/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('')