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
- Name: tin6150/circos
- License: None
View on Datalad
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://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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