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Last pushed: 24 days ago
Short Description
Automated build from reproducible_research_example Bitbucket repo.
Full Description

To reproduce all results in the presentation, choose one of the options below (A-E).

A. Clone this repo, install software manually, run scripts manually:

#!bash

$ git clone https://bitbucket.org/scilifelab-lts/reproducible_research_example.git
$ # the rest is up to you...

B. Clone this repo, install software manually:

#!bash

$ git clone https://bitbucket.org/scilifelab-lts/reproducible_research_example.git
$ cd reproducible_research_example
$ snakemake results/SRR068303.pdf

C. Clone this repo, use the conda environment file to facilitate software installation:

#!bash

$ git clone git clone https://bitbucket.org/scilifelab-lts/reproducible_research_example.git
$ cd reproducible_research_example
$ conda env create -f conda_env.yml
$ source activate my_conda_env
(my_conda_env)$ snakemake results/SRR068303.pdf

D. Clone this repo, build and run Docker image from Dockerfile:

#!bash

$ git clone https://bitbucket.org/scilifelab-lts/reproducible_research_example.git
$ cd reproducible_research_example
$ docker build -t "my_docker_image" .
$ docker run my_docker_image

E. Use the snapshot image of this repo + system + software from Docker hub:

#!bash

$ docker pull scilifelablts/reproducible_research_example:v1.0
$ docker run -it -v $PWD:/home/reproducible_research_example/results \
    scilifelablts/reproducible_research_example:v1.0 /bin/bash
root@27344a656192# cd reproducible_research_example
root@27344a656192# source activate my_conda_env
(my_conda_env)root@27344a656192# snakemake results/SRR068303.pdf
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scilifelablts