idia-container-sourcefinding-py3/sourcefinding_py3_update.def at master · idia-astro/idia-container-sourcefinding-py3 · GitHub

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Bootstrap: localimage
From: /mnt/containers/sourcefinding_py3_update/sourcefinding_py3-2018-08-30-tmp.simg
Include: software-properties-common

%environment

        export INSTALLER_PATH=/installer
        export SOFTWARE_PATH=/software
        export PATH=$SOFTWARE_PATH:$PATH
        export PATH="/anaconda3/bin:$PATH"
        export BLOBCAT_PATH=$INSTALLER_PATH/BLOBCAT
        export PATH=$BLOBCAT_PATH:$PATH

%setup
        #Copy patch file for blobcat
        cp blobcat_patch.diff $SINGULARITY_ROOTFS

%post

        # Create Installation Directories and export paths. This is needed as part of post.
        # %environment scriptlet does not define these paths during %post, only after.
        export INSTALLER_PATH=/installer
        export SOFTWARE_PATH=/software
        export PATH="/anaconda3/bin:$PATH"

        #Installation of BLOBCAT
        export BLOBCAT_PATH=$INSTALLER_PATH/BLOBCAT
        mkdir $BLOBCAT_PATH
        cd $BLOBCAT_PATH
        wget -O blobcat-v1.2.tar.bz2 http://sourceforge.net/projects/blobcat/files/blobcat-v1.2.tar.bz2/download
        tar xvjf blobcat-v1.2.tar.bz2

        #Patch blobcat to run python2.7 and fix error on one line
        patch blobcat.py /blobcat_patch.diff

        #Remove unneccesary files and change dir
        rm -f blobcat-v1.2.tar.bz2 /blobcat_patch.diff
        cd $INSTALLER_PATH

        #Upgrade pip
        pip install --upgrade pip

        #Installation of PASTA
        pip install git+https://github.com/bwkeller/PASTA

        #Update to PyBDSF for python3 (not currently working so don't overwrite working PyBDSF yet)
        #pip install git+https://github.com/lofar-astron/PyBDSF

        #Installation fits2hdf
        pip install git+https://github.com/telegraphic/fits2hdf

        #Installation of NOAO datalab client (for python2)
        pip2 install datalab-client

        #Install eog (and dependencies)
        apt-get -y install eog
        apt-get -yf install

        #Installation of PINK (not currently working - see standalone PINK container)
        #cd $INSTALLER_PATH
        #wget https://github.com/HITS-AIN/PINK/releases/download/1.1/Pink-1.1-Linux.deb
        #apt install -y ./Pink-1.1-Linux.deb

        # Install updated pprocess for Python 3 use by Aegean
        cd $INSTALLER_PATH
        wget -O - http://www.boddie.org.uk/python/downloads/pprocess-0.5.3.tar.gz | tar -xz
        cd pprocess-0.5.3
        2to3 -w .
        pip install --upgrade .

        #Installation of tensorflow with conda
        pip uninstall -y tensorflow
        conda install -y tensorflow

        #Install missing Astromatic software : https://www.astromatic.net (blindly copying previous syntax!)
        cd $INSTALLER_PATH
        wget https://www.astromatic.net/download/eye/eye-1.4.1.tar.gz -O - | tar -xz
        wget https://www.astromatic.net/download/missfits/missfits-2.8.0.tar.gz -O - | tar -xz
        wget https://www.astromatic.net/download/psfex/psfex-3.17.1.tar.gz -O - | tar -xz
        wget https://www.astromatic.net/download/skymaker/skymaker-3.10.5.tar.gz -O - | tar -xz
        wget https://www.astromatic.net/download/stiff/stiff-2.4.0.tar.gz -O - | tar -xz
        wget https://www.astromatic.net/download/stuff/stuff-1.26.0.tar.gz -O - | tar -xz
        wget https://www.astromatic.net/download/weightwatcher/weightwatcher-1.12.tar.gz -O - | tar -xz

        cd $INSTALLER_PATH/eye-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install
        cd $INSTALLER_PATH/missfits-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install
        cd $INSTALLER_PATH/psfex-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install
        cd $INSTALLER_PATH/skymaker-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install
        cd $INSTALLER_PATH/stiff-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install
        cd $INSTALLER_PATH/stuff-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install
        cd $INSTALLER_PATH/weightwatcher-*
        ./configure --with-atlas-incdir=/usr/include/atlas/ && make && make install

        #Update PUMA for python3 use
        cd $INSTALLER_PATH/PUMA
        git pull

        #Installation of pywcs tools (not currently working)
        #pip2 install --upgrade pip
        #pip2 install pywcs pywcsgrid2

        # Cleanup the container
        apt-get clean
        apt-get autoclean

%runscript

        /anaconda3/bin/python "$@"