rbrewster727/brewster_pipelines:sgv_finder
$ singularity pull shub://rbrewster727/brewster_pipelines:sgv_finder
Singularity Recipe
# Metagenomics Singularity environment definition for ICRA and SGV Finder
# Ryan Brewster
# rbrewster@stanford.edu
# June 2019
bootstrap: docker
from: ubuntu:19.04
# this command assumes at least singularity 2.3
%environment
PATH="/usr/local/anaconda/bin:$PATH"
%post
apt-get update
apt-get install -y eatmydata
eatmydata apt-get install -y wget bzip2 \
ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 \
git bc rsync zlib1g-dev libbz2-dev liblzma-dev autoconf
apt-get clean
apt-get install -y build-essential
# Install anaconda
if [ ! -d /usr/local/anaconda ]; then
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-O ~/anaconda.sh && \
bash ~/anaconda.sh -b -p /usr/local/anaconda && \
rm ~/anaconda.sh
fi
export PATH="/usr/local/anaconda/bin:$PATH"
conda install numpy=1.13.3 ujson=1.35 pandas=0.23.4 scipy=1.1.0 bokeh=0.12.6 python=2.7.8 cython
conda install -c conda-forge biopython=1.68 cxx-compiler
# Install GEM-Mapper
wget https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2
tar -jxvf GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2
rsync -r GEM-binaries-Linux-x86_64-core_i3-20130406-045632/bin/ /usr/bin/
Collection
- Name: rbrewster727/brewster_pipelines
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/rbrewster727-brewster_pipelines-sgv_finder |
collection name | rbrewster727/brewster_pipelines |
branch | master |
tag | sgv_finder |
commit | ae3f8ee3edd751d2b009ca89abdd38db67bca251 |
version (container hash) | ef2357cf4fc1b64aef854afbe0b8bc2c |
build date | 2019-06-24T14:48:03.806Z |
size (MB) | 2734 |
size (bytes) | 1247350815 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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