TomHarrop/align-utils:samtools_3389c09
$ singularity pull shub://TomHarrop/align-utils:samtools_3389c09
Singularity Recipe
Bootstrap: docker
From: ubuntu:19.10
%help
samtools 3389c09
bcftools d6d1ca6
htslib 2e36fa6
http://www.htslib.org/
%labels
VERSION "samtools 1.9"
%runscript
exec /usr/local/bin/samtools "$@"
%environment
export LC_ALL=C
%post
# faster apt downloads
export DEBIAN_FRONTEND=noninteractive
export LC_ALL=C
(
. /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
)
# apt dependencies
apt-get update
apt-get install -y \
build-essential \
git \
libbz2-dev \
libcurl4-openssl-dev \
liblzma-dev \
libncurses-dev \
wget \
zlib1g-dev
# install releases via github
git clone \
https://github.com/samtools/htslib.git \
/htslib
cd /htslib || exit 1
git checkout -f 2e36fa6
git submodule update --init --recursive
make
make install
git clone \
https://github.com/samtools/samtools.git \
/samtools
cd /samtools || exit 1
git checkout -f 3389c09
git submodule update --init --recursive
make
make install
git clone \
https://github.com/samtools/bcftools.git \
/bcftools
cd /bcftools || exit 1
git checkout -f d6d1ca6
git submodule update --init --recursive
make
make install
# tidy up
rm -rf /htslib /samtools /bcftools
Collection
- Name: TomHarrop/align-utils
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/TomHarrop-align-utils-samtools_3389c09 |
collection name | TomHarrop/align-utils |
branch | master |
tag | samtools_3389c09 |
commit | c874bc83c7148d34cb602932c67548d843540d4b |
version (container hash) | 370eb531d983aa59704e25c4fa91873e755319b4c2ea6e7e908dfb39f5beb4d4 |
build date | 2020-04-22T20:13:54.970Z |
size (MB) | 147.7109375 |
size (bytes) | 154886144 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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