dominik-handler/AP_singu:medakagpu
$ singularity pull shub://dominik-handler/AP_singu:medakagpu
Singularity Recipe
Bootstrap: docker
From: nvidia/cuda:10.0-cudnn7-runtime-ubuntu16.04
%labels
maintainer Dominik Handler <Dominik Handler@imba.oeaw.ac.at
medaka v1.0.0
%post
set -e
#fix locale
apt-get update
apt-get -y upgrade
apt-get install -y locales && rm -rf /var/lib/apt/lists/*
localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
export LC_COLLATE=C
#install dependencies
apt-get update
apt-get -y install software-properties-common
add-apt-repository universe
apt-get update
apt-get -y install bzip2 g++ zlib1g-dev libbz2-dev liblzma-dev libffi-dev libncurses5-dev libcurl4-gnutls-dev libssl-dev curl make cmake wget python3-all-dev python3-pip virtualenv git-core
#@ CUDA=10.0 CUDNN=7.4.1.5-1 /bin/bash
#@ apt-get -y install --no-install-recommends libcudnn7=7.5.1.10-1+cuda10.0
#@ python3 -m pip install --upgrade pip
#@ python3 -m pip install virtualenv
#install git-lfs
cd /tmp
wget --no-check-certificate --content-disposition https://github.com/git-lfs/git-lfs/releases/download/v2.11.0/git-lfs-linux-amd64-v2.11.0.tar.gz
tar -zxvf git-lfs-linux-amd64-v2.11.0.tar.gz
cat install.sh | sed 's/git lfs install/git lfs install --skip-repo/' > install_mod.sh
chmod 777 install_mod.sh
./install_mod.sh
#install medaka
cd /
git clone https://github.com/nanoporetech/medaka.git
cd medaka
sed -i 's/tar -xvf minimap2-${MINIMAPVER}_x64-linux.tar.bz2/tar -xvf minimap2-${MINIMAPVER}_x64-linux.tar.bz2 --no-same-owner /' Makefile
sed -i 's/tensorflow/tensorflow-gpu/' requirements.txt
make install
#clean up
apt-get autoremove
apt-get clean
%environment
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
export LC_COLLATE=C
. /medaka/venv/bin/activate
%runscript
medaka $@
Collection
- Name: dominik-handler/AP_singu
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dominik-handler-AP_singu-medakagpu |
collection name | dominik-handler/AP_singu |
branch | master |
tag | medakagpu |
commit | 131d3c72fe69e01c67a16d9d97950ce977ed0c37 |
version (container hash) | 9fa643e0573a5f41dd40441348d728c7bb7a9998242cd0476176373bbc9b39ba |
build date | 2020-06-17T11:33:40.119Z |
size (MB) | 2131.921875 |
size (bytes) | 2235482112 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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