TomHarrop/ont-containers:medaka_7574cf1
$ singularity pull shub://TomHarrop/ont-containers:medaka_7574cf1
Singularity Recipe
Bootstrap: docker
From: tensorflow/tensorflow:1.14.0-gpu-py3
%help
medaka 7574cf1
https://github.com/nanoporetech/medaka
%labels
MAINTAINER "Tom Harrop"
VERSION "medaka 7574cf1"
%post
# faster apt downloads, will it break?
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 ${UBUNTU_CODENAME}-security main restricted universe multiverse
_EOF_
mv /etc/apt/sources.list /etc/apt/sources.list.bak
cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
)
# dependencies
apt update
apt install -y \
cmake \
file \
git-lfs \
libbz2-dev \
libcurl4-openssl-dev \
liblzma-dev \
libncurses-dev \
libssl-dev \
virtualenv \
wget \
zlib1g-dev
# medaka gpu
GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/nanoporetech/medaka.git
cd medaka || exit 1
git checkout \
--recurse-submodules --force \
7574cf1
git lfs pull
sed -i 's/tensorflow/tensorflow-gpu/' requirements.txt
make install # this builds the binaries in bincache and installs into venv
# now install system-wide
/usr/local/bin/pip3 install -r requirements.txt
MEDAKA_BINARIES=1 python3 setup.py install
# tidy up
rm -r /medaka
%runscript
exec /usr/local/bin/medaka "$@"
Collection
- Name: TomHarrop/ont-containers
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/TomHarrop-ont-containers-medaka_7574cf1 |
collection name | TomHarrop/ont-containers |
branch | master |
tag | medaka_7574cf1 |
commit | 0a7f4c632e78b4c99afbe5b52a6838d01a0cabf3 |
version (container hash) | 2e10ba7f142261a1e87c66e4361b5ab6bb9088e2076037fd36111741be357ec3 |
build date | 2019-12-02T10:29:55.330Z |
size (MB) | 2146.4921875 |
size (bytes) | 2250760192 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.