Skip to content

Instantly share code, notes, and snippets.

Keith Bradnam kbradnam

Block or report user

Report or block kbradnam

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
kbradnam /
Last active May 4, 2016
Instructions for installing RepeatMasker on a server with Repbase database and RMBlast

Installing RepeatMasker on Mac OS X

Before we can install RepeatMasker itself, we need to install RMBlast, TRF (already installed on our server), and the repeat database Repbase. RepeatMasker also requires Perl 5.8.0 or higher.


RMBlast utilizes NCBI BLAST+ but you have to download a separate BLAST binary from NCBI. See the RMBlast page at RepeatMasker's website for details.

kbradnam /
Created May 23, 2014
Instructions for installing iPython by use miniconda

These instructions were originally provided by Michelle Gill and lightly adapted for our use.

Running this on lab server with sysadmin account

  1. cd /Volumes/Data/Korflab/Packages/
  2. mkdir Miniconda
  3. cd Miniconda
  4. Download the Python 2 version of Miniconda: curl -O
  5. Make executable: chmod +x
  6. Run script: sudo ./chmod +x
kbradnam / CVS_2_Git_
Created May 22, 2014
Converting old Korflab CVS repositories to Git repositories
View CVS_2_Git_

First install cvs2svn. This includes a cvs2git command. Then proceed to make dump files from the old repository (you must be on the korflab server machine at this point). The instructions to do this are taken from those on the cvs2svn website. Because we used one monolithic CVS repository for all projects, I used the following steps to migrate one CVS module at a time (not all CVS modules need to end up on GitHub):

For Assemblathon CVS repository

cd ~/Work/Code
mkdir cvs2git-tmp
cvs2git --blobfile=cvs2git-tmp/git-blob.dat --dumpfile=cvs2git-tmp/git-dump.dat --username=keith /Volumes/Data/cvsroot/Assemblathon/
git init Assemblathon
cd Assemblathon
kbradnam /
Created Apr 23, 2014
Find large FASTQ files over 100 MB in size and zip them
find . -name "*.fastq" -size 100M -exec gzip {} \;
kbradnam / 0_reuse_code.js
Created Apr 23, 2014
Here are some things you can do with Gists in GistBox.
View 0_reuse_code.js
// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console
You can’t perform that action at this time.