First working version for cnv_facets 0.16.0

CHANGELOG.md

@@ -7,31 +7,6 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
-## [Unreleased]
-### Changed
-- Changed something but it is not part of the last release.
-
----
-
-## [1.0.0] - YYYY-MM-DD
+## [0.16.0] - 2021-08-07
 ### Added
-- For new features.
-- Added item 1.
-
-### Changed
-- For changes in existing functionality.
-- Changed item 1.
-
-### Deprecated
-- For soon-to-be removed features.
-
-### Removed
-- For now removed features.
-- Removed item 1.
-
-### Fixed
-- For any bug fixes.
-- Fixed item 1.
-
-### Security
-- In case of vulnerabilities.
+- Dockerfile and documentation for cnv_facets

Dockerfile

@@ -1,14 +1,21 @@
 FROM blcdsdockerregistry/bl-base:1.0.0 AS builder
 
 # Use conda to install tools and dependencies into /usr/local
-ARG TOOL_VERSION=X.X.X
+ENV CNVFACETS_VERSION=0.16.0 \
+    SAMTOOLS_VERSION=1.9 \
+    MSCOREFONTS_VERSION=0.0.1
 RUN conda create -qy -p /usr/local \
-    -c bioconda \
-    -c conda-forge \
-    tool_name==${TOOL_VERSION}
+        -c bioconda \
+        -c conda-forge \
+        cnv_facets==${CNVFACETS_VERSION} \
+        samtools==${SAMTOOLS_VERSION} \
+        mscorefonts==${MSCOREFONTS_VERSION}
+
+# Install dependencies that are not properly handled by conda above
+RUN R -e 'install.packages("BiocManager", repos="http://cran.us.r-project.org"); BiocManager::install("GenomeInfoDbData")'
 
 # Deploy the target tools into a base image
 FROM ubuntu:20.04
 COPY --from=builder /usr/local /usr/local
 
-LABEL maintainer="Your Name <[email protected]>"
+LABEL maintainer="Cyriac Kandoth <[email protected]>"

README.md

@@ -1,25 +1,22 @@
-# docker-tool_name
-Template Repository for the Boutros Lab Dockerfiles based on the bl-base image.
+# docker-cnv_facets
+Dockerfile for [cnv_facets](https://github.com/dariober/cnv_facets), a convenient wrapper around [FACETS](https://github.com/mskcc/facets). This wrapper takes a tumor-normal pair of BAMs as input, and produces a VCF listing allele-specific copy-number variants.
 
-The bl-base image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/bl-base
+The image is located in the Boutros Lab Docker Hub repo: https://hub.docker.com/repository/docker/blcdsdockerregistry/cnv_facets
 
 # Documentation
-Docker introduction [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+Introduction)
+Guide to cnv_facets usage and results [here](https://github.com/dariober/cnv_facets/blob/master/README.md)
 
-Dockerfile Best Practices [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Dockerfile+Best+Practices)
-
-Docker image versioning standard [here](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Docker+image+versioning+standardization)
+Tips for setting `--cval` parameter [here](https://github.com/mskcc/facets/issues/76#issuecomment-385724786)
 
+Tips for understanding FACETS results [here](https://bandla-chai.gitbook.io/facets-preview/reviewing-fits#3-2-qc-summary)
 
 # Version
 | Tool | Version |
-|------|---------|
-|tool_name| X.X.X|
-|tool_name_2|X.X.X|
-
-
+|--------|-------|
+|cnv_facets|0.16.0|
 ---
 
 ## References
-
-1. Tool specific references can be listed here
+1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027494/
+2. https://github.com/mskcc/facets
+3. https://github.com/dariober/cnv_facets

metadata.yaml

@@ -1,10 +1,10 @@
 ---
 Category: 'docker'
-Description: 'Template Docker repository for tool_name'  # Description of why the repository exists
-Maintainers: ['YourName@mednet.ucla.edu']  # email address of maintainers
-Contributors: ['Your Name']  # Full names of contributors
-Languages: ['Dockerfile']  # programming languages used
-Tools: ['tool_name']  # Name of the tool(s) used in the Dockerfile
-Version: ['X.X.X']  # Tool version number
-Purpose of tool: ''  # Description of what this tool does
-References: ''  # is the tool/dependencies published, is there a confluence page
+Description: 'Docker repository for cnv_facets'
+Maintainers: ['ckandoth@mednet.ucla.edu']
+Contributors: ['Cyriac Kandoth']
+Languages: ['Dockerfile']
+Tools: ['cnv_facets']
+Version: ['0.16.0']
+Purpose of tool: 'Allele-specific somatic copy-number variant caller'
+References: 'https://github.com/dariober/cnv_facets'