kbradnam

A

Assemblathons ACGT

B

BIS180L

C

CEGMA Committee work

kbradnam

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

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

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 http://repo.continuum.io/miniconda/Miniconda-3.4.2-MacOSX-x86_64.sh
5. Make executable: chmod +x Miniconda-3.4.2-MacOSX-x86_64.sh
6. Run script: sudo ./chmod +x Miniconda-3.4.2-MacOSX-x86_64.sh

kbradnam

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

find . -name "*.fastq" -size  100M -exec gzip {} \;

kbradnam

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console