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Samir B. Amin dyndna

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Moved to @sbamin
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dyndna / diskstats.sh
Last active December 9, 2015 17:19
disk usage summary per user
#!/bin/bash
# Find disk usage per base directory, per user
# http://unix.stackexchange.com/a/77509/28675
# http://stackoverflow.com/a/32533111/1243763
BASEDIR="$1"
MYTIME="$(date +%d%b%y_%H%M%S%Z)"
if [ -z "$BASEDIR" ] || [ ! -d "$BASEDIR" ]; then
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dyndna / bed_to_gtf_pcawg14_gtf.md
Created May 21, 2015 19:05
bed to gtf conversion for PCAWG14 extended set of annotations

bed to gtf conversion for syn3606092 file, rnaseq.gc19_extNc.bed was done as follows:

Ref.: http://onetipperday.blogspot.com/2012/08/convert-bed-to-gtf.html

#wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToGenePred
#wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf
<workdir>/scripts/bedToGenePred rnaseq.gc19_extNc.bed rnaseq.gc19_extNc.btgp.genepred
<workdir>/scripts/genePredToGtf file rnaseq.gc19_extNc.btgp.genepred rnaseq.gc19_extNc.gptg.gtf
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dyndna / docker_config_dns_fix.md
Created May 20, 2015 21:12
Docker build "Could not resolve 'archive.ubuntu.com'" apt-get fails to install anything

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"

  1. Restart docker by sudo service docker restart or service restart command for other platforms.
  2. 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/
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dyndna / disable_bluetooth_ubuntu_1404.md
Created April 27, 2015 21:08
Disable bluetooth at startup in Ubuntu 14.04: From http://catlingmindswipe.blogspot.com/2012/05/how-to-disable-bluetooth-on-startup.html 
sudo cp /etc/bluetooth/main.conf /etc/bluetooth/main.conf.OLD
sudo nano /etc/bluetooth/main.conf

#Search for the entry:
InitiallyPowered = true

#and change the value to:
InitiallyPowered = false
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dyndna / circos_install_ubuntu_1404.md
Last active May 7, 2016 15:21
Install circos on ubuntu 14.04 LTS
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dyndna / docker_fix_centos.md
Created April 7, 2015 01:05
[Solved] docker does not run on cent os 6.6

Issue:

Upon sudo service docker start, docker daemon fails to start with tail /var/log/docker showing following error:

time="2015-04-07T00:28:43Z" level="info" msg="+job serveapi(unix:///var/run/docker.sock)" 
time="2015-04-07T00:28:43Z" level="info" msg="WARNING: You are running linux kernel version 2.6.32-504.12.2.el6.x86_64, which might be unstable running docker. Please upgrade your kernel to 3.8.0." 
time="2015-04-07T00:28:43Z" level="info" msg="Listening for HTTP on unix (/var/run/docker.sock)" 
time="2015-04-07T00:28:45Z" level="fatal" msg="Error loading device metadata file .tmp529617825"