diff --git a/singularity_conda.def b/singularity_conda.def new file mode 100644 index 0000000000000000000000000000000000000000..a4429044d39d25f38dffe82a404447eb9bcaff00 --- /dev/null +++ b/singularity_conda.def @@ -0,0 +1,36 @@ +BootStrap: docker +From: ubuntu:16.04 + +%post + # install some system deps + apt-get -y update + apt-get -y install locales curl bzip2 + locale-gen en_US.UTF-8 + apt-get clean + + # download and install miniconda2 + curl -sSL -O https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh + bash Miniconda2-latest-Linux-x86_64.sh -p /opt/miniconda2 -b + rm -fr Miniconda2-latest-Linux-x86_64.sh + + # use conda to install some bioinfo tools + conda install --yes -c bioconda samtools==1.7 + conda install --yes -c bioconda bwa=0.7.8 + +%environment + export LANG=en_US.UTF-8 + export LANGUAGE=en_US:en + export LC_ALL=en_US.UTF-8 + export PATH=/opt/miniconda2/bin:$PATH + +%apphelp samtools + "samtools version 1.7" + +%apprun samtools + /opt/miniconda2/bin/samtools + +%apphelp bwa + "BWA version 0.7.8" + +%apprun bwa + /opt/miniconda2/bin/bwa