Merge branch 'apptainer'

Author: yitzchak

apptainer/cando.def

@@ -0,0 +1,27 @@
+BootStrap: docker
+From: ubuntu:jammy
+
+%post
+    apt-get update
+    apt-get upgrade -y
+    apt-get install -y -o Dpkg::Options::="--force-overwrite" nano wget sudo git locales curl python3-pip nodejs npm binutils-gold clang-14 libclang-14-dev libfmt-dev libboost-dev libclang-cpp14-dev libelf-dev libgmp-dev libunwind-dev llvm-14 ninja-build sbcl pkg-config libnetcdf-dev libczmq-dev libexpat1-dev
+    echo 'en_US.UTF-8 UTF-8' >/etc/locale.gen
+    locale-gen
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    mkdir -p /home/cando/
+    chmod ugo+rwx /home/cando/
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /home/cando/miniconda3
+    rm -rf Miniconda3-latest-Linux-x86_64.sh
+    export PATH="/home/cando/miniconda3/bin:${PATH}"
+    conda install -y -c conda-forge jupyterlab ambertools
+    cd /mnt
+    ./koga --extensions=cando,seqan-clasp --build-path=build-apptainer/
+    ninja -C build-apptainer
+    ninja -C build-apptainer install
+    HOME=/home/cando cando-user-install
+    chmod -R ugo+rw /home/cando/
+
+%environment
+    export PATH="/home/cando/miniconda3/bin:${PATH}"
+    export AMBERHOME=/home/cando/miniconda3
+    export CLASP_QUICKLISP_DIRECTORY=/home/cando/quicklisp/  

apptainer/clasp.def

@@ -0,0 +1,16 @@
+BootStrap: docker
+From: ubuntu:jammy
+
+%post
+    apt-get update
+    apt-get upgrade -y
+    apt-get install -y -o Dpkg::Options::="--force-overwrite" nano wget sudo git locales curl python3-pip nodejs npm binutils-gold clang-14 libclang-14-dev libfmt-dev libboost-dev libclang-cpp14-dev libelf-dev libgmp-dev libunwind-dev llvm-14 ninja-build sbcl pkg-config libnetcdf-dev libczmq-dev libexpat1-dev
+    echo 'en_US.UTF-8 UTF-8' >/etc/locale.gen
+    locale-gen
+    cd /mnt
+    ./koga --build-path=build-apptainer/
+    ninja -C build-apptainer
+    ninja -C build-apptainer install
+
+%environment
+    export CLASP_QUICKLISP_DIRECTORY=/home/cando/quicklisp/