From 0f02ee0dea65af9654a3a2b8dfef6eb2f628f9af Mon Sep 17 00:00:00 2001
From: tefirman <tefirman@gmail.com>
Date: Mon, 25 Nov 2024 19:44:12 -0800
Subject: [PATCH] Adding STAR v2.7.4a

---
 star/Dockerfile_2.7.4a | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 star/Dockerfile_2.7.4a

diff --git a/star/Dockerfile_2.7.4a b/star/Dockerfile_2.7.4a
new file mode 100644
index 0000000..b5db4df
--- /dev/null
+++ b/star/Dockerfile_2.7.4a
@@ -0,0 +1,41 @@
+
+# Using the Ubuntu base image
+FROM ubuntu:oracular-20241009
+
+# Adding labels for the GitHub Container Registry
+LABEL org.opencontainers.image.title="star"
+LABEL org.opencontainers.image.description="Container image for the use of STAR in FH DaSL's WILDS"
+LABEL org.opencontainers.image.version="2.7.4a"
+LABEL org.opencontainers.image.authors="wilds@fredhutch.org"
+LABEL org.opencontainers.image.url=https://hutchdatascience.org/
+LABEL org.opencontainers.image.documentation=https://getwilds.org/
+LABEL org.opencontainers.image.source=https://github.com/getwilds/wilds-docker-library
+LABEL org.opencontainers.image.licenses=MIT
+
+# Installing prerequisites
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends build-essential=12.10ubuntu1 wget=1.24.5-1ubuntu2 \
+  zlib1g-dev=1:1.3.dfsg+really1.3.1-1ubuntu1 autoconf=2.72-3 automake=1:1.16.5-1.3ubuntu1 \
+  libncurses-dev=6.5-2 libbz2-dev=1.0.8-6 liblzma-dev=5.6.2-2 libssl-dev=3.3.1-2ubuntu2 \
+  libcurl4-gnutls-dev=8.9.1-2ubuntu2 xxd=2:9.1.0496-1ubuntu6 \
+  && rm -rf /var/lib/apt/lists/*
+
+# Pulling and extracting STAR source code
+RUN wget -q --no-check-certificate https://github.com/alexdobin/STAR/archive/2.7.4a.tar.gz && tar -xzf 2.7.4a.tar.gz
+
+# Installing STAR
+WORKDIR /STAR-2.7.4a/source
+RUN make STAR
+WORKDIR /
+ENV PATH="${PATH}:/STAR-2.7.4a/source"
+
+# Pulling and extracting Samtools source code
+RUN wget -q --no-check-certificate https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 && tar -jxf samtools-1.11.tar.bz2
+
+# Installing Samtools
+WORKDIR /samtools-1.11
+RUN ./configure && make && make install
+WORKDIR /
+
+# Cleanup
+RUN rm -rf samtools-1.11 samtools-1.11.tar.bz2