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Moved to @sbamin

Samir B. Amin dyndna

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Moved to @sbamin
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dyndna / slack_delfiles.py
Created June 6, 2016 22:16
Slack delete files older than n days
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 = ''
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dyndna / kallisto_install_fixes.md
Created May 11, 2016 02:52
Fix for errors on installing kallisto - cmake, GLIBCXX, GCC, LD LIBRARY PATHS

Install kallisto on HPC

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

@dyndna
dyndna / entrez_ensg_conversion.R
Created April 29, 2016 23:22
Convert between Ensembl gene ID and Entrez gene id/symbol
#### 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 )
@dyndna
dyndna / get_oauth2_token.py
Last active April 28, 2016 19:37 — forked from burnash/get_oauth2_token.py
Simple command line script to fetch a Google API's access token.
'''
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
@dyndna
dyndna / mpibzip2_makefile
Last active April 26, 2016 22:42
Makefile for mpibzip2: How to compile on cluster machine running Cent OS 6
#### 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
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dyndna / parse-options.sh
Created April 24, 2016 23:45 — forked from cosimo/parse-options.sh
Example of how to parse options with bash/getopt
#!/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"
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dyndna / tensorflow_in_r_using_rpython.R
Created March 24, 2016 20:28 — forked from rasmusab/tensorflow_in_r_using_rpython.R
An example of building a TensorFlow model from R using rPython
### 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... )
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dyndna / keybase.md
Created February 22, 2016 23:10

Keybase proof

I hereby claim:

  • I am dyndna on github.
  • I am sbamin (https://keybase.io/sbamin) on keybase.
  • I have a public key whose fingerprint is FC90 E95D 5E01 4D54 26FF 1163 13B4 0CB3 1EAE A07B

To claim this, I am signing this object:

@dyndna
dyndna / goglass.sh
Last active June 26, 2016 19:48
gists for blog posts
#!/bin/bash
# Wrapper to run docker based variant calling pipeline for GLASS consortium
# v1.0.2
# @sbamin @sethsa
# usage
show_help() {
cat << EOF
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dyndna / merge_bams_add_RG_CO_in_bam_header.md
Created January 28, 2016 23:36
Merge bam files using samtools merge, add @rg and @co tags in merged header file.

merge bams file and add @RG and @CO

Let's say you have two bam files from two different runs you need to merge.

  1. bam1_batch1.bam
  2. bam1_batch2.bam

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.