vignettes/Build-DockerContainer-for-kallisto.md

In teamcgc/cgcR: NCI Cancer Genomics Cloud examples in R

title: "Kallisto-docker-container" author: "Durga Addepalli" date: "June 16, 2016" output: html_document

```{r include=FALSE} knitr::opts_chunk$set(eval = TRUE)

## INTRODUCTION
This guide will walk you through the steps to build a docker container for the tool "kallisto". kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.You can read more about [Kallisto] here:(https://pachterlab.github.io/kallisto/)
(https://github.com/pachterlab/kallisto)

This tutorial assumes you have the docker installed and running.For documentation on docker installation refer to [Using Docker] (https://github.com/teamcgc/cgcR/blob/master/vignettes/UsingDocker.Part1.Rmd)

First lets copy the kallisto git repository from Github to any of your local folder!

git clone https://github.com/InSilicoDB/docker-kallisto.git kallisto-test

Move into the dicretory created

cd kallisto-test

Build a new image from the source code in this directory with the name 'kallisto' and version '0'

docker build -t kallisto:v0 .

Once the build is done, you will need to get the Image id of the container and run the following command to be able to run kallisto

docker run -it kallisto:v0

Push the image to docker hub

docker push durgaadd/kallisto:v0

Run kallisto by running the docker image, this will get you to the bash command prompt of the kallisto container

docker run -it kallisto:v0

## Mounting a volume (mounitng a local directory onto the docker container, for getting input files to run kallisto)

To mount a local directory onto the docker container, we need to edit the Docker file and add the following RUN command

vi Dockerfile RUN mkdir -p /tmp/files

Specify the local directory with input data files

docker run -itv :/mnt/files kallisto:v0

Now inside the container (looks like root@<containerID>....), you can check to see the files/directory

cd /mnt/files

```

Related Tutorials

Install Docker Toolbox on Mac OS X

teamcgc/cgcR documentation built on May 31, 2019, 7:56 a.m.