From 6b85cf4c1896626a78d5a0052723f42e80ce2c47 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Thu, 7 Dec 2023 18:24:15 -0500
Subject: [PATCH] Adding CNVkit and sequenza to CNV docker image

---
 docker/genome-seek/cnv/Dockerfile | 21 ++++++++++++++++++++-
 docker/genome-seek/cnv/README.md  | 12 ++++++------
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/docker/genome-seek/cnv/Dockerfile b/docker/genome-seek/cnv/Dockerfile
index deb7da6..f444888 100644
--- a/docker/genome-seek/cnv/Dockerfile
+++ b/docker/genome-seek/cnv/Dockerfile
@@ -4,7 +4,7 @@
 FROM skchronicles/genome-seek:v0.1.0
 LABEL maintainer="Skyler Kuhn <kuhnsa@nih.gov>" \
     base_image="skchronicles/genome-seek:v0.1.0" \
-    version="v0.2.0"   \
+    version="v0.3.0"   \
     software="genome-seekq cnv" \
     about.summary="An awesome Clinical Whole Genome Sequencing Pipeline" \
     about.home="https://github.com/OpenOmics/genome-seek" \
@@ -153,6 +153,25 @@ RUN mkdir -p /opt2/slivar/0.3.0/bin \
     && chmod a+x /opt2/slivar/0.3.0/bin/slivar
 ENV PATH="${PATH}:/opt2/slivar/0.3.0/bin"
 
+# Install cnvkit/0.9.10, for more info see:
+# https://github.com/etal/cnvkit
+# Requires python>=3.7 and for extended
+# functionality, requires the following 
+# R package from Bioconductor: "DNAcopy",
+# python3 version and DNAcopy requirement
+# already satified, cnvkit/0.9.10 not compatiable
+# with pomegranate>=1.0.0, see for more info: 
+# https://github.com/etal/cnvkit/issues/815
+RUN pip3 install pomegranate==0.14.9 && pip3 install cnvkit==0.9.10
+
+# Installs sequenza/3.0.0, for more info see:
+# https://cran.r-project.org/web/packages/sequenza/index.html
+# Requires R, Python, SAMtools, tabix (already satisfied)
+# https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#getting-started
+RUN pip3 install sequenza-utils==3.0.0 \
+      && Rscript -e 'install.packages(c("pbapply", "squash", "iotools", "seqminer"), repos="http://cran.r-project.org");' \
+      && Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/sequenza/sequenza_3.0.0.tar.gz", repos=NULL, type="source")'
+
 
 ################ POST #################
 # Add Dockerfile and export env variables
diff --git a/docker/genome-seek/cnv/README.md b/docker/genome-seek/cnv/README.md
index 910c078..a2abde0 100644
--- a/docker/genome-seek/cnv/README.md
+++ b/docker/genome-seek/cnv/README.md
@@ -9,20 +9,20 @@ Directly below are instructions for building an image using the provided Dockerf
 docker image ls
 
 # Build from Dockerfile
-docker build --no-cache -f Dockerfile --tag=genome-seek_cnv:v0.2.0 .
+docker build --no-cache -f Dockerfile --tag=genome-seek_cnv:v0.3.0 .
 
 # Testing, take a peek inside
-docker run -ti genome-seek_cnv:v0.2.0 /bin/bash
+docker run -ti genome-seek_cnv:v0.3.0 /bin/bash
 
 # Updating Tag  before pushing to DockerHub
-docker tag genome-seek_cnv:v0.2.0 skchronicles/genome-seek_cnv:v0.2.0
-docker tag genome-seek_cnv:v0.2.0 skchronicles/genome-seek_cnv         # latest
+docker tag genome-seek_cnv:v0.3.0 skchronicles/genome-seek_cnv:v0.3.0
+docker tag genome-seek_cnv:v0.3.0 skchronicles/genome-seek_cnv         # latest
 
 # Check out new tag(s)
 docker image ls
 
 # Push new tagged image to DockerHub
-docker push skchronicles/genome-seek_cnv:v0.2.0
+docker push skchronicles/genome-seek_cnv:v0.3.0
 docker push skchronicles/genome-seek_cnv:latest
 ```
 
@@ -31,7 +31,7 @@ docker push skchronicles/genome-seek_cnv:latest
 Scan your image for known vulnerabilities:
 
 ```bash
-docker scan genome-seek_cnv:v0.2.0
+docker scan genome-seek_cnv:v0.3.0
 ```
 
 > **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.