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

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

#!/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

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

#!/usr/bin/env python2.7
import sys, os.path
import subprocess
import time
import lockfile
import threading

lock = lockfile.FileLock(os.path.join(os.path.expanduser("~"), ".delay"))
lock.acquire()

mschubert

#
# loading the table, converting it to an expression matrix
#
df = read.table(
    "GBM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.data.txt",
    header=TRUE, sep="\t", stringsAsFactors=FALSE)
expr = data.matrix(df[2:nrow(df), df[1,]=="raw_count"])
rownames(expr) = df[2:nrow(df), 1]

#

mschubert

#BSUB-J {{ job_name }}                    # name of the job / array jobs
#BSUB-o {{ log_file | /dev/null }}        # output is sent to logfile, stdout + stderr by default
#BSUB-P {{ queue }}                       # Job queue
#BSUB-W {{ walltime }}                    # Walltime in minutes
#BSUB-M {{ memory | 4096 }}               # Memory requirements in Mbytes
#BSUB-R rusage[mem={{ memory | 4096  }}]  # Memory requirements in Mbytes
#BSUB-R select[panfs_nobackup_research]

R --no-save --no-restore --args "{{ args }}" < "{{ rscript }}"

mschubert

# Consider the following setup:
#
# root
# + a
# | + Makefile 
# | + ..some other files..
# + b
#   + Makefile
#   + ..some other files..
#

mschubert

# ignore system installation
# e.g. https://github.com/EBI-predocs/research-software/issues/57
.libPaths("~/.R")

# no factor coercion
# no graphical package install menu
# warn if partial matching arguments
options(
    stringsAsFactors = FALSE,

mschubert

n = 1:1e7

# use a loop
new_n = rep(NA, length(n))
for (i in seq_along(n))
    new_n[i] = n[i] * 2 - 5

# use *apply
new_n = sapply(n, function(x) x * 2 - 5)