dyndna

Docker build "Could not resolve 'archive.ubuntu.com'" apt-get fails to install anything

In Ubuntu Precise 12.04 LTS, after executing docker build command, e.g., docker build -t myimages/pcawg3_1 -f ./icgc_rnaseq_align/, build engine may halt at step 1: apt-get with errors similar to Could not resolve 'archive.ubuntu.com'. This is occurring most likely because of inability of docker ubuntu image to resolve apt-get urls with default Google DNS.

To resolve this issue: [Ref. http://stackoverflow.com/a/24991137]

1. Uncomment following line in /etc/default/docker, and preferably replace Google DNS with those from your own ISP:

DOCKER_OPTS="--dns 8.8.8.8 --dns 8.8.4.4"

2. Restart docker by sudo service docker restart or service restart command for other platforms.
3. Reissue docker build, and add no-cache=true flag to force docker image fetch new DNS, e.g., docker build --no-cache=true -t myimages/pcawg3_2 -f ./icgc_rnaseq_align/

dyndna

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.

dyndna

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

#!/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"

dyndna

#!/bin/bash

# Wrapper to run docker based variant calling pipeline for GLASS consortium
# v1.0.2
# @sbamin @sethsa

# usage
show_help() {
cat << EOF

dyndna

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 = ''

dyndna

Download Circos:

http://circos.ca/software/download/

wget http://circos.ca/distribution/circos-0.67-7.tgz
tar xvzf circos-0.67-7.tgz
cd circos-0.67-7/bin
ls

dyndna

#### 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

'''
    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

#### 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