https://github.com/nci-gdc/muse-tool
GDC MuSE docker
https://github.com/nci-gdc/muse-tool
bioinformatics docker workflow-tool
Last synced: about 1 month ago
JSON representation
GDC MuSE docker
- Host: GitHub
- URL: https://github.com/nci-gdc/muse-tool
- Owner: NCI-GDC
- License: apache-2.0
- Created: 2016-01-07T00:04:12.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2025-07-11T18:14:03.000Z (11 months ago)
- Last Synced: 2025-07-11T20:26:50.266Z (11 months ago)
- Topics: bioinformatics, docker, workflow-tool
- Language: Python
- Homepage:
- Size: 507 KB
- Stars: 0
- Watchers: 8
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# GDC MuSE
[](https://travis-ci.com/NCI-GDC/muse-tool)
`merge-muse`: [](https://quay.io/repository/ncigdc/merge-muse)
`muse-tool`: [](https://quay.io/repository/ncigdc/muse-tool)
`multi-muse`: [](https://quay.io/repository/ncigdc/multi-muse)
MuSE is somatic point mutation caller developed by Dr. Wenyi Wang’s group in MD Anderson Cancer Center (MDACC), and used by the Human Genome Sequencing Center (HGSC) in the Baylor College of Medicine (BCM). Thus it is often referred to as the Baylor pipeline. This pipeline takes a pair of tumor and normal BAM files, and does two-step calling and summarization to generate somatic SNV and INDEL VCFs. The only auxiliary file requirement is a VCF file from Single Nucleotide Polymorphism Database (dbSNP) for annotation.
Original MuSE: http://bioinformatics.mdanderson.org/main/MuSE
## How to build
https://docs.docker.com/engine/reference/builder/
The docker images are tested under multiple environments. The most tested ones are:
* Docker version 19.03.2, build 6a30dfc
* Docker version 18.09.1, build 4c52b90
* Docker version 18.03.0-ce, build 0520e24
* Docker version 17.12.1-ce, build 7390fc6
## For external users
The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in [GDC reference files](https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files "GDC reference files"). For any questions related to GDC data, please contact the GDC Help Desk at support@nci-gdc.datacommons.io.
There is a production-ready CWL example at https://github.com/NCI-GDC/muse-cwl which uses the docker images that are built from the `Dockerfile`s in this repo.
To use docker images directly or with other workflow languages, we recommend to build and use either MuSE or multi-threading MuSE call.
To run multi-threading MuSE call:
```
docker run -it {YOUR DOCKER} muse_tool multi
```
or
```
python3.9 multi_muse.py
```
```
usage: Internal multithreading MuSE call. [-h] -f REFERENCE_PATH -r
INTERVAL_BED_PATH -t TUMOR_BAM -n
NORMAL_BAM -c THREAD_COUNT
[--muse-binary MUSE_BINARY]
optional arguments:
-h, --help show this help message and exit
-f REFERENCE_PATH, --reference_path REFERENCE_PATH
Reference path.
-r INTERVAL_BED_PATH, --interval_bed_path INTERVAL_BED_PATH
Interval bed file.
-t TUMOR_BAM, --tumor_bam TUMOR_BAM
Tumor bam file.
-n NORMAL_BAM, --normal_bam NORMAL_BAM
Normal bam file.
-c THREAD_COUNT, --thread_count THREAD_COUNT
Number of threads.
--muse-binary MUSE_BINARY
Path to MuSE binary
```
## For GDC users
See https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow.