mbhall88/Singularity_recipes:fast5
$ singularity pull shub://mbhall88/Singularity_recipes:fast5
Singularity Recipe
Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%environment
PATH=/usr/local/bin:$PATH
%post
apt-get update
apt-get install -y software-properties-common wget
apt-add-repository universe
apt-get update
# ================================
# INSTALL FAST5 LIBRARY
# ================================
FAST5_VERSION=0.6.5
apt-get install -y build-essential libhdf5-dev libpython2.7-dev \
python2.7-minimal python-pip
# install python dependencies for fast5 lib
wget https://bootstrap.pypa.io/get-pip.py -O - | \
python - && \
pip install cython setuptools virtualenv
# expose prerequisites settings and make available at runtime
export HDF5_INCLUDE_DIR=/usr/include/hdf5/serial/
export HDF5_LIB_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial/
echo 'export HDF5_INCLUDE_DIR=/usr/include/hdf5/serial/' >> $SINGULARITY_ENVIRONMENT
echo 'export HDF5_LIB_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial/' >> $SINGULARITY_ENVIRONMENT
# download and install version release from GitHub
RELEASE_URL=https://github.com/mateidavid/fast5/archive/v${FAST5_VERSION}.tar.gz
wget "$RELEASE_URL" -O - | tar xzf -
cd fast5-${FAST5_VERSION}/python
python setup.py install
Collection
- Name: mbhall88/Singularity_recipes
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mbhall88-Singularity_recipes-fast5 |
collection name | mbhall88/Singularity_recipes |
branch | master |
tag | fast5 |
commit | 3e798dfd6fcd56aa9957b0cd6c512f7039d87cef |
version (container hash) | 161cf10a9eaeca33e78b6fb75548ce70 |
build date | 2020-05-15T06:50:45.744Z |
size (MB) | 844 |
size (bytes) | 403726367 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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