mkweskin

#Create new env with conda libgcc
conda create -n ORFfinder -c anaconda libgcc
source activate ORFfinder

#Setup scripts to set LD_LIBRARY_PATH
mkdir -p $CONDA_PREFIX/etc/conda/activate.d
mkdir -p $CONDA_PREFIX/etc/conda/deactivate.d

cat <<EOF >$CONDA_PREFIX/etc/conda/activate.d/LD_PATH.sh
export LD_LIBRARY_PATH_CONDA_BACKUP=$LD_LIBRARY_PATH

mkweskin

while [ 1 ]; do date; ping -o -q -t 3 x.x.x.x >/dev/null && echo PASS || echo FAIL; sleep 5; done >~/pinglog

mkweskin

Linux find

find is used to find files based on their name or other attributes of the file.

• It does not search inside files like the grep command
• To find find examples for a speicific purpose, I do a web search for: linux find ...

Basic find command: search for a filename

find /path/to/dir -iname '*text*'

Dissecting this:

• /path/to/dir: where you want to search, I often use . for my current directory

mkweskin

#!/usr/bin/env python3
import sqlite3
import sys
import shutil
import os

#Existing DB
exist="probe.matches.sqlite"

#To be added DB

mkweskin

#!/usr/bin/env python3

import pandas as pd
from Bio import SeqIO
import argparse
import os
import logging
import sys
import datetime

mkweskin

pandoc -f gfm -w jira -o outfile.jira infile.md

# To import converted file into Confluence:
#  - Create new page
#  - Click on the body of the page, click on the " + \/" dropdown in toolbar ("Insert more content") and select "Markup"
#  - Paste the contents into the pop-up window (select "Confluence wiki" as the format)
#     - Note: The "Markdown" option in the import pop-up doesn't seem to work for Github flavored markdown (gfm).

mkweskin

My preferred settings for PuTTY (0.71)

• Terminal

  • Bell
    • Action to happen when a bell occurs : None (bell disabled)

• Window

  • Lines of scrollback: 50000
  • Appearance

• Font : Courier Std, 12 pt

mkweskin

#!/usr/bin/env python3

"""
Author: Matthew Kweskin, github: @mkweskin

This script converts the sequence names in a FASTA file
to the md5 hash of the sequence.

Notes:
- Gaps will automatically be removed by biopython

mkweskin

#!/usr/bin/env python3

"""
Author: Matthew Kweskin, github: @mkweskin

A general utility to read in a delimited translation file with two columns
and rename any text file with these values.
"""

import argparse

mkweskin

Bootstrap: docker

From: continuumio/miniconda3

%post
/opt/conda/bin/conda config --add channels defaults
/opt/conda/bin/conda config --add channels bioconda
/opt/conda/bin/conda config --add channels conda-forge
/opt/conda/bin/conda config --add channels omnia
/opt/conda/bin/conda config --add channels plotly