INSTALL.md

#sequencing_utilities

##Douglas McCloskey

##Credits:

Ali Ebrahim for writing the original sequtil library from which this is derived

###Installation using Docker:

1. Install docker

2. at the command terminal, enter "docker pull dmccloskey/sequencing_utilities" to download the docker image from the dmccloskey dockerhub repo

(Currently, there appears to be an issue with pushes of large image files to the dockerhub repository. For now, the best way of generating the docker image is using the command "docker build -t dmccloskey/sequencing_utilities" while in a local directory with the Dockerfile (e.g., cd Dockerbuild where the Dockerbuild directory would contain only the Dockerfile).)

3. at the command terminal, enter "docker run -i -t --name=sequtils dmccloskey/sequencing_utilities" to bring up an interactive python session in a newly created docker container

###Installation from individual packages:

1. Install R

2. Install python and dependencies

3. Install Bowtie, Bowtie2, Breseq, Samtools, and Cufflinks

###Dependencies:

Python 3.4+

Bowtie

Bowtie2

Breseq

Samtools

Cufflinks

R 3.01+

Python-dependencies:

pysam

numpy

scipy

rpy2

...

(see Dockerfile for a complete list of all packages and dependencies)