From 53d035f097c596d02a8173b78a9569a80847f528 Mon Sep 17 00:00:00 2001
From: Simon <simondonaldmurray@gmail.com>
Date: Thu, 13 Apr 2023 13:43:20 +0100
Subject: [PATCH] added dockerfile

---
 Dockerfile | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 README.md  |  1 +
 2 files changed, 60 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..6612e08
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,59 @@
+FROM ubuntu:20.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG star_version=2.7.10a_alpha_220818
+ARG samtools_version=1.15.1
+ARG bbmap_version=38.97
+ARG rsem_version=1.3.3
+
+#Install OS packages
+RUN apt-get update && apt-get -y --no-install-recommends -qq install \
+    wget gcc build-essential software-properties-common libz-dev \
+    git libncurses5-dev libbz2-dev liblzma-dev default-jre bsdmainutils
+
+#Install STAR
+RUN wget --no-check-certificate https://github.com/alexdobin/STAR/archive/${star_version}.tar.gz && \
+    tar -xzf ${star_version}.tar.gz -C /opt && \
+    cd /opt/STAR-${star_version}/source && \
+    make STAR CXXFLAGS_SIMD="-msse4.2" && \
+    cd / && rm ${star_version}.tar.gz 
+
+#Install seqtk
+RUN git clone https://github.com/lh3/seqtk.git && \
+    mv seqtk /opt && \
+    cd /opt/seqtk && \
+    make
+
+#Install samtools
+RUN wget https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2 && \
+    tar -xvf samtools-${samtools_version}.tar.bz2 -C /opt && \
+    cd /opt/samtools-${samtools_version} && \
+    ./configure && \
+    make && \
+    make install && \
+    cd / && rm samtools-${samtools_version}.tar.bz2  
+
+#Install BBMap
+RUN wget https://sourceforge.net/projects/bbmap/files/BBMap_${bbmap_version}.tar.gz && \
+    tar -xzf BBMap_${bbmap_version}.tar.gz -C /opt && \
+    cd /opt/bbmap && \
+    ./stats.sh in=resources/phix174_ill.ref.fa.gz && \
+    cd / && rm BBMap_${bbmap_version}.tar.gz
+
+#Install RSEM
+RUN wget https://github.com/deweylab/RSEM/archive/refs/tags/v${rsem_version}.tar.gz && \
+    tar -xzf v${rsem_version}.tar.gz -C /opt && \
+    cd /opt/RSEM-${rsem_version} && \
+    make && \
+    cd / && rm v${rsem_version}.tar.gz
+
+ENV PATH="${PATH}:/opt/STAR-${star_version}/source:/opt/seqtk:/opt/bbmap:/opt/RSEM-${rsem_version}"     
+
+#Saving Software Versions to a file
+RUN echo "STAR version: ${star_version}" >> versions.txt && \
+    echo "samtools version: ${samtools_version}" >> versions.txt && \
+    echo "BBMap version: ${bbmap_version}" >> versions.txt && \
+    echo "RSEM version: ${rsem_version}" >> versions.txt && \
+    seqtk_version=`strings $(which seqtk) | grep 'Version:' | cut -f 2 -d " "` && \
+    echo "seqtk version: ${seqtk_version}" >> versions.txt 
diff --git a/README.md b/README.md
index f37fc7c..06e3821 100644
--- a/README.md
+++ b/README.md
@@ -15,6 +15,7 @@ There are two branches:
 * `bin/solo_QC.sh` - a quick qc script that enables quick sanity checks that STARsolo worked correctly.
 * `bin/cram2fastq_10x.sh` - a script that converts CRAM files (usual storage type at Sanger) to fastq files. This pipeline expects CRAM files for each sample stored internally on Sanger irods that are accessed using a custom `myrods.sh` script. TO DO - update this to not use myrods.
 * `bin/starsolo_10x_auto.sh` - a script that runs STARsolo outputting: exonic, exonic+intronic and velocyto results.
+* `Dockerfile` - a dockerfile to reproduce the environment used to run the pipeline.
 
 ## Pipeline Arguments:
 * `--SAMPLEFILE` - The path to the sample file provided to the pipeline which contains one sample ID per line. This sample is assumed to have CRAM files stored on IRODS.