rmcolq/Singularity_recipes:nanosimh
$ singularity pull shub://rmcolq/Singularity_recipes:nanosimh
Singularity Recipe
Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%help
A container to hold the read simulator nanosim.
Run `singularity exec nanosim.simg nanosim`
%environment
PATH=/usr/local/bin:$PATH
%post
apt-get update
apt-get install -y --no-install-recommends apt-utils
apt-get update
apt-get install -y software-properties-common
apt-add-repository universe
apt-get update
apt-get install -y \
automake \
build-essential \
cmake \
git \
gnuplot \
graphviz \
openjdk-8-jre \
libbz2-dev \
libfreetype6-dev \
libhts-dev \
liblzma-dev \
libncurses5-dev \
libncursesw5-dev \
pkg-config \
python3-dev \
python3-pip \
python3-setuptools \
python3-tk \
python3-venv \
samtools \
tabix \
vcftools \
wget \
zlib1g-dev
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
echo 'export LC_ALL=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
echo 'export LANG=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
#============================================
# INSTALL MINIMAP2
#============================================
VERSION="2.15"
wget https://github.com/lh3/minimap2/archive/v"$VERSION".tar.gz
tar xzf v"$VERSION".tar.gz
rm v"$VERSION".tar.gz
cd minimap2-*
make
export PATH=$PWD:$PATH
echo "export PATH=$(pwd):$PATH" >> $SINGULARITY_ENVIRONMENT
cd ..
#============================================
# INSTALL NANOSIM
#============================================
git clone https://github.com/karel-brinda/nanosim-h
cd nanosim-h
python3 setup.py install
Collection
- Name: rmcolq/Singularity_recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/rmcolq-Singularity_recipes-nanosimh |
collection name | rmcolq/Singularity_recipes |
branch | master |
tag | nanosimh |
commit | 9ad025c10ab23e5da73a7661f0aff6ffebce2836 |
version (container hash) | 69a5428353c2cd1cdda300f809879ea0 |
build date | 2019-01-31T21:34:12.219Z |
size (MB) | 1441 |
size (bytes) | 632369183 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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