diff --git a/biostats_mcgee/Dockerfile b/biostats_mcgee/Dockerfile index 57c21c4c..87470048 100644 --- a/biostats_mcgee/Dockerfile +++ b/biostats_mcgee/Dockerfile @@ -9,12 +9,38 @@ LABEL maintainer="Robert Kalescky " ENV DEBIAN_FRONTEND noninteractive RUN apt-get update &&\ - apt-get install -y\ - libz-dev\ - default-jre\ + apt-get remove -y libcurl4 &&\ + apt-get upgrade -y &&\ + apt-get install -y --no-install-recommends\ + apt-transport-https\ + autoconf\ + ca-certificates\ + cmake\ + curl\ default-jdk\ - python3-pip - + default-jre\ + g++\ + gcc\ + git\ + git-lfs\ + gnupg\ + libboost-all-dev\ + libbz2-dev\ + libcereal-dev\ + libcurl4-openssl-dev\ + libgff-dev\ + libjemalloc-dev\ + liblzma-dev\ + libtbb-dev\ + libz-dev\ + make\ + ninja-build\ + python3-pip\ + software-properties-common\ + unzip\ + wget\ + zlib1g-dev + # FastQC RUN git clone --depth 1 --branch v0.11.9\ https://github.com/s-andrews/FastQC.git /opt/FastQC &&\ @@ -47,3 +73,17 @@ RUN git clone --depth 1 --branch v1.3.3\ COPY install_packages.R / RUN Rscript /install_packages.R +# GATK4 +RUN git clone --depth 1 --branch 4.2.6.1\ + https://github.com/broadinstitute/gatk.git /opt/gatk &&\ + cd /opt/gatk &&\ + ./gradlew installAll + +# Salmon +RUN git clone --depth 1 --branch v1.9.0\ + https://github.com/COMBINE-lab/salmon.git /opt/salmon &&\ + mkdir /opt/salmon/build &&\ + cd /opt/salmon/build &&\ + cmake .. &&\ + make install + diff --git a/biostats_mcgee/biostats.lua b/biostats_mcgee/biostats.lua index c7b25e45..03007a73 100644 --- a/biostats_mcgee/biostats.lua +++ b/biostats_mcgee/biostats.lua @@ -1,6 +1,6 @@ load("singularity") -local img_name = 'biostats_latest-2023-01-27-60654e0170ff.simg' +local img_name = 'biostats_latest-2023-02-07-858e2914ccfc.sif' local img_directory = '/hpc/applications/containers/' local img_path = pathJoin(img_directory, img_name)