tin6150/circos:latest

$ singularity pull shub://tin6150/circos:latest

Singularity Recipe

# Singularity container definition hosting tool from circos.ca in CentOS 6 env
#
# Circos installed in /opt, contain examples and tutorials.  
# xv graphics viewer included to see generated .png, doesn't work for .svg
# This image need to be at least 1200 MB 
# adopted from  https://singularity-hub.org/collections/98/
# https://github.com/tin6150/circos/Singularity

BootStrap:docker
From:centos:6
 
# yum bootstrap method didn't work in singularity-hub ca 2017.04
# which, gcc, gawk wget not installed ... 
# BootStrap: yum
# OSVersion: 6
# MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
# Include: yum

%runscript
    /opt/circos/circos-0.69-6/bin/circos 

%post
    yum -y install bash
    yum -y install wget
    yum -y install curl
    yum -y install tar              # circos extract
    yum -y install coreutils        # for convinience, provide yes
    yum -y install which            # for debugging use only, not req
    yum -y install vim
    yum -y install util-linux-ng    # u/mount, etc
    yum -y install gawk             # circos ./list.modules 
    yum -y install gcc              # some cpan modules need gcc (eg Clone)
    yum -y install gd
    #yum -y install eog             # throws DBus error :(
    yum -y install perl
    yum -y install perl-CPAN
    yum -y install perl-CPANPLUS
    yum -y install perl-GD          # no TTF support ??
    wget -nc https://raw.githubusercontent.com/tin6150/singhub/master/circos_perl_mod.sh
    bash circos_perl_mod.sh
    CIRCOS_DIR=/opt/circos
    CIRCOS_VER=0.69-6
    CIRCOS_TOOLS_VER=0.22
    CIRCOS_TUTORIAL_VER=0.67
    CIRCOS_SOURCE_FILE=circos-${CIRCOS_VER}
    CIRCOS_TOOLS_SOURCE_FILE=circos-tools-${CIRCOS_TOOLS_VER}
    CIRCOS_TUTORIAL_SOURCE_FILE=circos-tutorials-${CIRCOS_TUTORIAL_VER}
    test -d $CIRCOS_DIR || mkdir -p $CIRCOS_DIR
    cd $CIRCOS_DIR
    wget -nc "http://circos.ca/distribution/${CIRCOS_SOURCE_FILE}.tgz"
    wget -nc "http://circos.ca/distribution/${CIRCOS_TOOLS_SOURCE_FILE}.tgz"
    wget -nc "http://circos.ca/distribution/${CIRCOS_TUTORIAL_SOURCE_FILE}.tgz"
    tar xfz ${CIRCOS_SOURCE_FILE}.tgz
    tar xfz ${CIRCOS_TOOLS_SOURCE_FILE}.tgz
    tar xfz ${CIRCOS_TUTORIAL_SOURCE_FILE}.tgz
    touch       ${CIRCOS_SOURCE_FILE}/example/run.out 
    chmod 777   ${CIRCOS_SOURCE_FILE}/example/run.out 
    chmod -R a+w ${CIRCOS_TUTORIAL_SOURCE_FILE}/* 
    echo 'PATH=$PATH:'"${CIRCOS_DIR}/${CIRCOS_SOURCE_FILE}/bin;" 'export PATH' >> /etc/profile
    echo 'PATH=$PATH:'"${CIRCOS_DIR}/${CIRCOS_SOURCE_FILE}/bin;" 'export PATH' >> /etc/bashrc

    # optional XV graphics viewer - shareware (eog don't work due to DBus error)
    XV_PKG_FILE=xv-3.10a-37.el6.x86_64.rpm
    cd /tmp
    wget ftp://fr2.rpmfind.net/linux/atrpms/el6-x86_64/atrpms/stable/${XV_PKG_FILE} 
    rpm -i ${XV_PKG_FILE}
    rm     ${XV_PKG_FILE}

Collection


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Metrics

key value
id /containers/tin6150-circos-latest
collection name tin6150/circos
branch docker
tag latest
commit d793adb4dca974c250c7c2a310cad807234bc345
version (container hash) 265f23de0661046de700372b3c31ecda
build date 2019-10-15T18:06:38.513Z
size (MB) 1012
size (bytes) 513335327
SIF Download URL (please use pull with shub://)
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Singularity Recipe Singularity Recipe on Datalad
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