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February 2, 2026 07:28
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A sample Singularity.def script
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| BootStrap: debootstrap | |
| OSVersion: bionic | |
| MirrorURL: http://us.archive.ubuntu.com/ubuntu/ | |
| %runscript | |
| echo "This is what happens when you run the container..." | |
| %post | |
| echo "Hello from inside the container" | |
| apt-get -y update | |
| apt-get -y upgrade | |
| apt-get -y dist-upgrade | |
| apt-get install cmake -y | |
| apt-get update; | |
| apt-get install -y software-properties-common | |
| #apt-get install add-apt-repository | |
| apt-get update | |
| apt-get install git -y | |
| apt-get install libboost-all-dev -y | |
| apt-get update && apt-get install -y linux-tools-generic | |
| apt-get install wget curl | |
| git clone https://github.com/samtools/htslib.git | |
| cd htslib/ | |
| git submodule update --init --recursive | |
| autoreconf -i | |
| ./configure | |
| make | |
| make install | |
| cd .. | |
| wget https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2 | |
| tar -xvjf samtools-1.12.tar.bz2 | |
| cd samtools-1.12/ | |
| ./configure #--prefix=/usr/local/bin/ | |
| make | |
| make install | |
| git clone https://github.com/lh3/bwa.git | |
| cd bwa | |
| make | |
| mv bwa /usr/local/bin | |
| apt-get clean | |
| %environment | |
| export PATH=$PATH:/usr/local/bin |
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