cd kallisto-0.42.5/build
cmake ..
-- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.4.7 -- Check for working C compiler: /usr/bin/cc
import urllib | |
import urllib2 | |
import time | |
import json | |
#Credit: https://gist.github.com/jackcarter/d86808449f0d95060a40 and | |
# https://gist.github.com/jackcarter/d86808449f0d95060a40#gistcomment-1755139 | |
# put oauth test token between '' | |
token = '' |
#### Get gene annotations #### | |
# By Michael Love, http://www.bioconductor.org/help/workflows/rnaseqGene/ | |
library("AnnotationDbi") | |
library("org.Hs.eg.db") | |
columns(org.Hs.eg.db) | |
convertIDs <- function( ids, from, to, db, ifMultiple=c("putNA", "useFirst")) { | |
stopifnot( inherits( db, "AnnotationDb" ) ) | |
ifMultiple <- match.arg( ifMultiple ) |
''' | |
This script will attempt to open your webbrowser, | |
perform OAuth 2 authentication and print your access token. | |
It depends on two libraries: oauth2client and gflags. | |
To install dependencies from PyPI: | |
$ pip install python-gflags oauth2client | |
#### Parallel MPI BZIP2 | |
## See man doc at http://compression.ca/mpibzip2/ | |
### for .tar or tar.bz2 files, | |
## mpirun -np 4 mpibzip2 myfile.tar or mpirun -np 4 mpibzip2 myfile.tar.bz2 | |
### for tar.gz files, see pigz at http://serverfault.com/a/270825/149084 | |
## pigz -dk -p 4 target.tar.gz | tar -xf | |
# remove -k to delete original file after decompression. | |
# Make file for MPI BZIP2 | |
SHELL=/bin/sh |
#!/bin/bash | |
# | |
# Example of how to parse short/long options with 'getopt' | |
# | |
OPTS=`getopt -o vhns: --long verbose,dry-run,help,stack-size: -n 'parse-options' -- "$@"` | |
if [ $? != 0 ] ; then echo "Failed parsing options." >&2 ; exit 1 ; fi | |
echo "$OPTS" |
### An example of building a TensorFlow model from R using rPython ### | |
# For this script you need to | |
# 1. Have python 2.7 installed. | |
# 2. Install the rPython package in R. | |
# 3. Install Google's TensorFlow library as per these instructions: | |
# http://www.tensorflow.org/get_started/os_setup.md#binary_installation | |
### Here is how to setup and run a trivial TensorFlow model ### | |
# Load TensorFlow (I couldn't get this to work without setting sys.argv... ) |
I hereby claim:
To claim this, I am signing this object:
#!/bin/bash | |
# Wrapper to run docker based variant calling pipeline for GLASS consortium | |
# v1.0.2 | |
# @sbamin @sethsa | |
# usage | |
show_help() { | |
cat << EOF |
Let's say you have two bam files from two different runs you need to merge.
Using samtools view -H <bamfile>
, get @RG information for each of two bams. I usually get ID, DT and PL info. from bam header and then add SM (sample tag) tag using following script. You can run this script before samtools merge
command in your PBS script.