mbhall88/Singularity_recipes:medaka
$ singularity pull shub://mbhall88/Singularity_recipes:medaka
Singularity Recipe
Bootstrap: shub
from: mbhall88/Singularity_recipes:template
%post
apt install -y curl zlib1g-dev libbz2-dev liblzma-dev libffi-dev libncurses5-dev \
libcurl4-gnutls-dev libssl-dev python3-all-dev python-virtualenv python3-pip
# install samtools
VERSION="1.9"
URL="https://github.com/samtools/samtools/releases/download/${VERSION}/samtools-${VERSION}.tar.bz2"
wget "$URL" -O - | tar -jxf -
cd samtools* || exit 1
./configure --prefix=/usr/local
make
make install
cd "$HOME" || exit 1
# install minimap2
VERSION="2.11"
URL=https://github.com/lh3/minimap2/releases/download/v${VERSION}/minimap2-${VERSION}_x64-linux.tar.bz2
wget "$URL" -O - | tar -jxf -
cd minimap2-${VERSION}_x64-linux/ || exit 1
echo "export PATH=$(pwd):$PATH" >> $SINGULARITY_ENVIRONMENT
# install medaka
VERSION="0.7.1"
pip3 install medaka=="$VERSION"
Collection
- Name: mbhall88/Singularity_recipes
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mbhall88-Singularity_recipes-medaka |
collection name | mbhall88/Singularity_recipes |
branch | master |
tag | medaka |
commit | fc132841cea261394da0b6c6f4faf8e530ac0f33 |
version (container hash) | 120cf5e0782611095c716747692ac9f2 |
build date | 2019-06-02T17:47:33.068Z |
size (MB) | 1610 |
size (bytes) | 646836255 |
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.