Public | Automated Build

Last pushed: 6 months ago
Short Description
Docker image for the sequenza tumor-normal SCNA tools. Includes BWA, samtools, tabix, R and pypy
Full Description



Sequenza workflow

Allele-specific SCNA analysis from tumor/normal sequencing with the sequenza docker container

Dockstore

Use this sample sequenza_cwl.json with public URLs for sample data.

   $ dockstore tool launch --entry registry.hub.docker.com/sequenza/sequenza  --json sequenza_cwl.json

More information and instruction are available in the tool dockstore.org project page.

Interactive in Docker

Add some data to a folder in the host:

ls -1 input/
    subset.fa.gz
    subset.gc50.gz
    testnorm.bam
    testtum.bam

Mount the folder in docker

(It is possible to mount also an output folder, but on OSX I had permission problems)

docker run -ti \
   -v `pwd`/input:/input \
   sequenza:latest bash

Look around

ls /input

sequenza-pipeline --help

Run the pipeline in docker

sequenza-pipeline \
       --sample-id test_seq_doc \
       --normal-bam  /input/testnorm.bam \
       --tumor-bam /input/testtum.bam \
       --reference-gz /input/subset.fa.gz

results in the /home/docker/*

Building

You need Docker installed in order to perform this build.

cd sequenza_docker
docker build -t sequenza .
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Owner
sequenza
Source Repository