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Microtest test data

Microtest is a repository of small test data from various data types, for testing pipelines.

Data descriptions

(please include here a short description of any data files you add)

  • bs_aln_k1k3.bam: Bisulfite data aligned to the methylated/unmethylated spike-in control sequences (k1/k3).
  • wgbs1.bam/wgbs2.bam: Random samples of unaligned WGBS data.

Usage

With looper/pypiper in a virtualev

# create and activate a virtual environment
virtualenv microtestenv --no-site-packages; cd microtestenv; . ./bin/activate

# install the stack
pip install https://github.com/epigen/looper/zipball/master
pip install https://github.com/epigen/pypiper/zipball/master

# clone open_pipelines and microtest
git clone https://github.com/epigen/open_pipelines
git clone https://github.com/epigen/microtest

# run
export CODE=`pwd`
# run only tutorial pipeline (no additional dependecies)
looper run --file-checks microtest/config/microtest_config.tutorial.yaml

# or run all (would require additional software dependecies)
looper run --file-checks microtest/config/microtest_config.tutorial.yaml

Single pipeline usage

AMPLICON=`sed 's/,/\t/g' microtest/config/microtest_annotation.tutorial.csv | tail -n 1 | cut -f 14`
GUIDE=`sed 's/,/\t/g' microtest/config/microtest_annotation.tutorial.csv | tail -n 1 | cut -f 15`

python open_pipelines/pipelines/amplicon_simple.py \
-S microtest_amplicon -i microtest/data/amplicon.fastq.gz -g $GUIDE -a $AMPLICON -O microtes_amplicon

Test data production

How samples were made:

samtools view -s .0001 sample.bam -b > new_sample.bam

Automatic testing with a Github hook

  1. Open a listening port for webhooks:
    1. Get ngrok at https://ngrok.com and open a port: ./ngrok 3456
    2. add that URL + "/payload" to the github webhook with a secret key
  2. Create a listening server:
    1. git clone git@github.com:afrendeiro/github-webhook-handler.git
    2. modify github-webhook-handler/repos.json with your repositories that should trigger the testing and the secret key(s)
    3. start the server and leave it running: python github-webhook-handler/index.py 4567

When there is a push to your repositories, run_microtest.sh will run. This creates an isolated virtual environment, installs dependencies (not pipeline-specific ones though!) and runs the pipelines on the microtest data (similar to the example above).