From 57b49a9114644dbb7c4788a648556f4ab326979b Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Wed, 20 Mar 2024 11:24:53 -0400
Subject: [PATCH] Chore: adding umap to latest docker image

---
 docker/cfchip_toolkit/latest            |  1 +
 docker/cfchip_toolkit/v0.5.0/Dockerfile | 34 ++++++++++++++++++++++++
 docker/cfchip_toolkit/v0.5.0/README.md  | 35 +++++++++++++++++++++++++
 3 files changed, 70 insertions(+)
 create mode 120000 docker/cfchip_toolkit/latest
 create mode 100644 docker/cfchip_toolkit/v0.5.0/Dockerfile
 create mode 100644 docker/cfchip_toolkit/v0.5.0/README.md

diff --git a/docker/cfchip_toolkit/latest b/docker/cfchip_toolkit/latest
new file mode 120000
index 0000000..48080b4
--- /dev/null
+++ b/docker/cfchip_toolkit/latest
@@ -0,0 +1 @@
+v0.5.0
\ No newline at end of file
diff --git a/docker/cfchip_toolkit/v0.5.0/Dockerfile b/docker/cfchip_toolkit/v0.5.0/Dockerfile
new file mode 100644
index 0000000..5fdfb51
--- /dev/null
+++ b/docker/cfchip_toolkit/v0.5.0/Dockerfile
@@ -0,0 +1,34 @@
+# Dockerfile for cfChIP Toolkit
+# https://www.nature.com/articles/s41587-020-00775-6
+# Uses Ubuntu Focal (20.04 LTS) as base image
+# https://github.com/OpenOmics/chrom-seek/commit/48c3903261fe1c5979b2f6b62beb03cbd62c7468
+FROM skchronicles/cfchip_toolkit:v0.4.0
+LABEL maintainer="Skyler Kuhn <kuhnsa@nih.gov>" \
+    base_image="skchronicles/cfchip_toolkit:v0.3.0" \
+    version="v0.5.0"   \
+    software="chrom-seek_cfchip_toolkit" \
+    about.summary="An awesome set of Epigenetic Pipeline" \
+    about.home="https://github.com/OpenOmics/chrom-seek" \
+    about.documentation="https://openomics.github.io/chrom-seek/" \
+    about.tags="cell-free ChIP-seq"
+
+############# OVERVIEW ##################
+# Adds the following packages:
+#  • R/4.X
+#    - umap              (CRAN)
+
+
+############### INSTALL #################
+# Extra packages for differential bind
+# analysis in the cfChIP pipeline 
+WORKDIR /opt2
+RUN Rscript -e 'install.packages(c("umap"), repos="http://cran.r-project.org")'
+
+
+################ POST ###################
+# Add Dockerfile and export env variables
+RUN mv /opt2/Dockerfile /opt2/cfchip_toolkit-v0.5.0.dockerfile
+ADD Dockerfile /opt2/Dockerfile
+RUN chmod -R a+rX /opt2 
+ENV PATH="/opt2:$PATH"
+WORKDIR /data2
diff --git a/docker/cfchip_toolkit/v0.5.0/README.md b/docker/cfchip_toolkit/v0.5.0/README.md
new file mode 100644
index 0000000..228bb2d
--- /dev/null
+++ b/docker/cfchip_toolkit/v0.5.0/README.md
@@ -0,0 +1,35 @@
+## Steps for Building Docker Images
+
+Directly below are instructions for building a base image for the `cfchip_toolkit` using the provided Dockerfile:
+
+```bash
+# See listing of images on computer
+docker image ls
+
+# Build from Dockerfile
+docker build --no-cache -f Dockerfile --tag=cfchip_toolkit:v0.5.0 .
+
+# Testing, take a peek inside
+docker run -ti cfchip_toolkit:v0.5.0 /bin/bash
+
+# Updating Tag  before pushing to DockerHub
+docker tag cfchip_toolkit:v0.5.0 skchronicles/cfchip_toolkit:v0.5.0
+docker tag cfchip_toolkit:v0.5.0 skchronicles/cfchip_toolkit         # latest
+
+# Check out new tag(s)
+docker image ls
+
+# Push new tagged image to DockerHub
+docker push skchronicles/cfchip_toolkit:v0.5.0
+docker push skchronicles/cfchip_toolkit:latest
+```
+
+### Other Recommended Steps
+
+Scan your image for known vulnerabilities:
+
+```bash
+docker scan cfchip_toolkit:v0.5.0
+```
+
+> **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.