mschubert

// gcc -DZMQ_BUILD_DRAFT_API=ON -lzmq -o test_monitor test_monitor.c
// ./test_monitor

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <zmq.h>

void recv_print(void *frontend) {
    zmq_msg_t message;

mschubert

" install plug by
" curl -fLo ~/.local/share/nvim/site/autoload/plug.vim --create-dirs \
"    https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim

" expand tab with 4 spaces
set expandtab
set shiftwidth=4
set tabstop=4
set smarttab
set autoindent

mschubert

# Download ICGC public release in a semi-automated manner
#
# Usage: ./download_icgc.sh
#
# Be sure to check the original link to contain all summary files
#   https://dcc.icgc.org/releases/release_23/Summary
# and list all files you want from the cohorts in contents().
#
# There may be different contents in the project folders. Check a couple, e.g.:
#   https://dcc.icgc.org/releases/release_23/Projects/CLLE-ES

mschubert

# enable line editing for terminal
if [ -t 1 ]; then
    bind '"\e[A": history-search-backward'
    bind '"\e[B": history-search-forward'
fi

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)

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

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

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

#
# 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

#!/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()