icaoberg/singularity-bioformats:latest

$ singularity pull shub://icaoberg/singularity-bioformats:latest

Singularity Recipe

Bootstrap: docker
From: debian:latest

IncludeCmd: yes

%labels
    AUTHOR icaoberg
    EMAIL icaoberg@alumni.cmu.edu
    WEBSITE http://linus.cbd.cs.cmu.edu

%runscript
    exec /bin/bash "$@"

%post
    /usr/bin/apt-get update && apt-get install -y --no-install-recommends apt-utils
    /usr/bin/apt-get update --fix-missing
    /usr/bin/apt-get install -y unzip wget default-jre ffmpeg imagemagick

    #install bio-formats cli tools
    wget -nc https://downloads.openmicroscopy.org/bio-formats/6.2.1/artifacts/bftools.zip
    unzip bftools.zip -d /opt
    rm -f bftools.zip

####################################################################################
#  _     _              __                            _
# | |__ (_) ___        / _| ___  _ __ _ __ ___   __ _| |_ ___
# | '_ \| |/ _ \ _____| |_ / _ \| '__| '_ ` _ \ / _` | __/ __|
# | |_) | | (_) |_____|  _| (_) | |  | | | | | | (_| | |_\__ \
# |_.__/|_|\___/      |_|  \___/|_|  |_| |_| |_|\__,_|\__|___/
####################################################################################
%appenv showinf
    APP=/opt/bftools/showinf
    export APP

%apphelp showinf
    /opt/bftools/showinf --help

%apprun showinf
    /opt/bftools/showinf "$@"

%appenv ijview
    APP=/opt/bftools/ijview
    export APP

%apphelp ijview
    /opt/bftools/ijview --help

%apprun ijview
    /opt/bftools/ijview "$@"

%appenv bfconvert
    APP=/opt/bftools/bfconvert
    export APP

%apphelp bfconvert
    /opt/bftools/bfconvert --help

%apprun bfconvert
    /opt/bftools/bfconvert "$@"

%appenv formatlist
    APP=/opt/bftools/formatlist
    export APP

%apphelp formatlist
    /opt/bftools/formatlist --help

%apprun formatlist
    /opt/bftools/formatlist "$@"

%appenv xmlindent
    APP=/opt/bftools/xmlindent
    export APP

%apphelp xmlindent
    /opt/bftools/xmlindent --help

%apprun xmlindent
    /opt/bftools/xmlindent "$@"

%appenv xmlvalid
    APP=/opt/bftools/xmlvalid
    export APP

%apphelp xmlvalid
    /opt/bftools/xmlvalid --help

%apprun xmlvalid
    /opt/bftools/xmlvalid "$@"

%appenv tiffcomment
    APP=/opt/bftools/tiffcomment
    export APP

%apphelp tiffcomment
    /opt/bftools/tiffcomment --help

%apprun tiffcomment
    /opt/bftools/tiffcomment "$@"

%appenv domainlist
    APP=/opt/bftools/domainlist
    export APP

%apphelp domainlist
    /opt/bftools/domainlist --help

%apprun domainlist
    /opt/bftools/domainlist "$@"
####################################################################################

#################################################################################### 
#    __  __
#  / _|/ _|_ __  _ __   ___  __ _
# | |_| |_| '_ \| '_ \ / _ \/ _` |
# |  _|  _| | | | |_) |  __/ (_| |
# |_| |_| |_| |_| .__/ \___|\__, |
#               |_|         |___/
####################################################################################
%apphelp ffmpeg
    ffmpeg --help

%apprun ffmpeg
    ffmpeg "$@"
####################################################################################

####################################################################################
#  ___                            __  __             _      _
# |_ _|_ __ ___   __ _  __ _  ___|  \/  | __ _  __ _(_) ___| | __
#  | || '_ ` _ \ / _` |/ _` |/ _ \ |\/| |/ _` |/ _` | |/ __| |/ /
#  | || | | | | | (_| | (_| |  __/ |  | | (_| | (_| | | (__|   <
# |___|_| |_| |_|\__,_|\__, |\___|_|  |_|\__,_|\__, |_|\___|_|\_\
#                      |___/                   |___/
####################################################################################
%apphelp magick
    magick --help

%apprun magick
    magick "$@"

%apphelp animate
    animate --help

%apprun animate
    animate "$@"

%apphelp compare
    compare --help

%apprun compare
    compare "$@"

%apphelp composite
    composite --help

%apprun composite
    composite "$@"

%apphelp conjure
    conjure --help

%apprun conjure
    conjure "$@"

%apphelp convert
    convert --help

%apprun convert
    convert "$@"

%apphelp display
    display --help

%apprun display
    display "$@"

%apphelp identify
    identify --help

%apprun identify
    identify "$@"

%apphelp mogrify
    mogrify --help

%apprun mogrify
    mogrify "$@"

%apphelp montage
    montage --help

%apprun montage
    montage "$@"
####################################################################################

Collection

• Name: icaoberg/singularity-bioformats
• License: None

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