mschubert

library(stringr)
library(BatchJobs)
library(plyr)

# Rationale
#  This script uses BatchJobs to run functions either locally, on multiple cores, or LSF,
#  depending on your BatchJobs configuration. It has a simpler interface, does more error
#  checking than the library itself, and is able to queue different function calls. The
#  function supplied *MUST* be self-sufficient, i.e. load libraries and scripts.
#  BatchJobs on the EBI cluster is already set up when using the gentoo prefix.

mschubert

#!/bin/bash
# Script to (decrypt encfs and) selectively sync a remote sshfs directory
 
REMOTEDIR=server:/path/to/some/encfs
LOCALDIR=/path/to/local/directory

MOUNTFUNC=_ssh+encfs 

# verbose
# set -vx

mschubert

# a unix-like pipe operator in R to perform CLI operations (or call R functions)
`%|%` = function(x, command) {
    if (class(command) == 'function') {
        command(x)
    } else {
        stopifnot(class(x) %in% c('character', 'numeric', 'integer'))
        system(command, input=as.character(x), intern=TRUE)
    }
}

mschubert

#!/usr/bin/env python
"""
Fake qsub command, for testing qsub jobs in local

original: https://bitbucket.org/dalloliogm/fake-qsub
"""

import argparse
import subprocess
import logging