diff --git a/README b/README index bf4c7930862160c195a5f24bb7f7c92f692ad342..d53fb0fbf7f314c331976117c0f413a6f3e44435 100644 --- a/README +++ b/README @@ -46,8 +46,8 @@ AUTHOR VERSION - 0.6.2 + 0.6.3 LAST UPDATED - Tuesday, January 15th, 2019 + Friday, January 18th, 2019 diff --git a/definition-files/comet/jupyter/jupyter-cpu.def b/definition-files/comet/jupyter/jupyter-cpu.def new file mode 100644 index 0000000000000000000000000000000000000000..defb6dd5afb8118f937645a4e340e0995524835a --- /dev/null +++ b/definition-files/comet/jupyter/jupyter-cpu.def @@ -0,0 +1,137 @@ +Bootstrap: debootstrap +MirrorURL: http://us.archive.ubuntu.com/ubuntu +OSVersion: xenial + +%labels + + APPLICATION_NAME jupyter + APPLICATION_VERSION 4.4.0 + APPLICATION_URL https://www.ubuntu.com/ + + SYSTEM_NAME comet + SYSTEM_SINGULARITY_VERSION 2.5.2 + SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html + + SINGULARITY_IMAGE_SIZE 4096 + + AUTHOR_NAME Marty Kandes + AUTHOR_EMAIL mkandes@sdsc.edu + + LAST_UPDATED 20190118 + +%setup + +%environment + + # Set system locale + export LC_ALL=C + export PATH="/opt/miniconda3/bin:${PATH}" + +%post -c /bin/bash + + # Set system locale + export LC_ALL=C + + # Install system metapackages + apt-get -y install ubuntu-standard + apt-get -y install ubuntu-server + + # Add repositories + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted" + + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted" + + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted" + + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse" + add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted" + + # Upgrade all packages to their latest versions + apt-get -y update && apt-get -y upgrade + + # Install common packages from 'main' + apt-get -y install autoconf + apt-get -y install automake + apt-get -y install build-essential + apt-get -y install cmake + apt-get -y install libtool + apt-get -y install pkg-config + apt-get -y install gfortran + apt-get -y install zip + + # Install expect to automate responses for interactive build questions + apt-get -y install expect + + # Make filesystem mount points + mkdir /cvmfs /oasis /projects /scratch + + # Use /tmp to store temporary files within the container during the + # bootstraping process + cd /tmp + + # Install miniconda2 + wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh + chmod +x Miniconda2-latest-Linux-x86_64.sh + ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2 + + # Install miniconda3 + wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh + chmod +x Miniconda3-latest-Linux-x86_64.sh + ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3 + + # Install common python(2) packages for data science and machine + # learning applications + export PATH="/opt/miniconda2/bin:${PATH}" + conda install -y numpy + conda install -y mkl + conda install -y mkl-include + conda install -y pandas + conda install -y matplotlib + conda install -y ipython + conda install -y ipython-notebook + conda install -y jupyter + conda install -y sympy + conda install -y nose + conda install -y scikit-learn + conda install -y scikit-image + conda install -y nltk + conda install -y statsmodels + conda install -y opencv + + # Install common python3 packages for data science and machine + # learning applications + export PATH="/opt/miniconda3/bin:${PATH}" + conda install -y numpy + conda install -y mkl + conda install -y mkl-include + conda install -y pandas + conda install -y matplotlib + conda install -y ipython + conda install -y jupyter + conda install -y sympy + conda install -y nose + conda install -y scikit-learn + conda install -y scikit-image + conda install -y nltk + conda install -y statsmodels + conda install -y opencv + + # Update database for mlocate + updatedb + +%files + +%runscript + +%test diff --git a/naked-singularity.sh b/naked-singularity.sh index 4be5adf456e93440628b24eeafd47da1ef518370..1b0923b518554aacfb6e475a9cd877638deef8df 100755 --- a/naked-singularity.sh +++ b/naked-singularity.sh @@ -72,7 +72,7 @@ naked_build() { naked_out "Read in command-line option '${1}' with input value '${2}' ... " case "${1}" in -s | --system ) - system="${2,,}" + system="${2}" shift 2 ;; -a | --application )