vals

lindenb

/**

distribution of distance between variants. Non-Variant, Filterer or GVCF blocks are ignored

usage:
 java -jar jvarkit-git/dist/bioalcidae.jar -f distance.js input.vcf | sort -k1,1g | uniq -c


*/
var prev=null;

Brainiarc7

Transient compute clustering with GNU Parallel and sshfs:

GNU Parallel is a multipurpose program for running shell commands in parallel, which can often be used to replace shell script loops,find -exec, and find | xargs. It provides the --sshlogin and --sshloginfile options to farm out jobs to multiple hosts, as well as options for sending and retrieving static resources and and per-job input and output files.

For any particular task, however, keeping track of which files need to pushed to and retrieved from the remote hosts is somewhat of a hassle. Furthermore, cancelled or failed runs can leave garbage on the remote hosts, and if input and output files are large, sending them to local disk on the remote hosts is somewhat inefficient.

In a traditional cluster, this problem would be solved by giving all nodes access to a shared filesystem, usually with NFS or something more exotic. However, NFS doesn't wo

Brainiarc7

GNU Parallel for Bioinformatics: A primer

Installation:

A quick installation does not require root access, as shown:

(wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash

For other installation options see http://git.savannah.gnu.org/cgit/parallel.git/tree/README

bsmith89

*.ipynb	filter=dropoutput_jupyter
*.[tc]sv	diff=daff-csv
*.[tc]sv	merge=daff-csv

dianjuar

Fix a stop job is running for session c2 of user xxx (xs / 1min 30s)

This advice is pointing to arch based distributions. Manjaro in special

Install watchdog

# pacman -S watchdog >

josteink

On why stateful code is bad
===========================

STUDENT: Sir, can I ask a question?
TEACHER: Yes!
STUDENT: How do you put an elephant inside a fridge?
TEACHER: I don't know.
STUDENT: It's easy, you just open the fridge and put it in. I have another question!
TEACHER: Ok, ask.
STUDENT: How to put a donkey inside the fridge?

kantale

#!/usr/bin/python

import sys

'''
Just a simple tool that adds the line number at
the end of each line
'''

with open(sys.argv[1]) as f_in, open(sys.argv[2], 'w') as f_out:

anmoljagetia

#!/usr/bin/env bash
# Base16 - Gnome Terminal color scheme install script

[[ -z "$PROFILE_NAME" ]] && PROFILE_NAME="terminal.flat.theme"
[[ -z "$PROFILE_SLUG" ]] && PROFILE_SLUG="terminal-flat-theme"
[[ -z "$DCONF" ]] && DCONF=dconf
[[ -z "$UUIDGEN" ]] && UUIDGEN=uuidgen

dset() {
    local key="$1"; shift

nl5887

function transfer
    if test (count $argv) -eq 0
        echo "No arguments specified. Usage:\necho transfer /tmp/test.md\ncat /tmp/test.md | transfer test.md"
        return 1
    end

    ## get temporarily filename, output is written to this file show progress can be showed
    set tmpfile ( mktemp -t transferXXX )

    ## upload stdin or file