TomHarrop/assembly-utils:purge_haplotigs_0b9afdf
$ singularity pull shub://TomHarrop/assembly-utils:purge_haplotigs_0b9afdf
Singularity Recipe
Bootstrap: docker
From: ubuntu:19.10
%help
Container for purge_haplotigs
https://bitbucket.org/mroachawri/purge_haplotigs
%labels
VERSION "purge_haplotigs 0b9afdf"
%post
# faster apt downloads
export DEBIAN_FRONTEND=noninteractive
(
. /etc/os-release
cat << _EOF_ > mirror.txt
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME} main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-security main restricted universe multiverse
_EOF_
mv /etc/apt/sources.list /etc/apt/sources.list.bak
cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
)
# dependencies
apt-get update
apt-get install -y \
bedtools \
build-essential \
git \
minimap2 \
samtools \
wget
# install r separately to prevent X11 installation
apt install --no-install-recommends -y \
r-cran-ggplot2
# install mummer
# wget -O "mummer.tar.gz" \
# --no-check-certificate \
# https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz
# mkdir mummer-install
# tar -zxf mummer.tar.gz \
# -C mummer-install \
# --strip-components 1
# cd mummer-install || exit 1
# ./configure && make && make install
# cd .. || exit 1
# rm -rf mummer.tar.gz mummer-install
# ldconfig
# clone
git clone https://bitbucket.org/mroachawri/purge_haplotigs.git
cd purge_haplotigs || exit 1
git checkout -f 0b9afdf
git submodule update --init --recursive
%environment
export LC_ALL=C
export PATH="${PATH}:/purge_haplotigs/bin"
%runscript
exec /purge_haplotigs/bin/purge_haplotigs "$@"
Collection
- Name: TomHarrop/assembly-utils
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/TomHarrop-assembly-utils-purge_haplotigs_0b9afdf |
collection name | TomHarrop/assembly-utils |
branch | master |
tag | purge_haplotigs_0b9afdf |
commit | ad516825fc3d222c63acdb393daf2a68bf6ce136 |
version (container hash) | 232155e0d28b07cc3db7d5dc18fd9644b060dcb36902c549918f47c87ddb46e5 |
build date | 2020-06-17T07:27:02.051Z |
size (MB) | 284.3125 |
size (bytes) | 298123264 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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