rmcolq/Singularity_recipes:pilon
$ singularity pull shub://rmcolq/Singularity_recipes:pilon
Singularity Recipe
Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%help
A container to hold the polishing tool pilon.
Run `singularity exec pilon.simg pilon`
%environment
PATH=/usr/local/bin:$PATH
%post
apt-get update
apt-get install -y software-properties-common
apt-add-repository universe
apt-get update
apt-get install -y \
build-essential \
cmake \
git \
libbz2-dev \
liblzma-dev \
libncurses-dev \
openjdk-8-jre \
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' >> $SINGULARITY_ENVIRONMENT
#============================================
# INSTALL MINIMAP2
#============================================
VERSION="2.11"
wget https://github.com/lh3/minimap2/archive/v"$VERSION".tar.gz
tar xzf v"$VERSION".tar.gz
rm v"$VERSION".tar.gz
cd minimap2-*
make
echo "export PATH=$PWD:$PATH" >> $SINGULARITY_ENVIRONMENT
cd ..
#================================
# INSTALL SAMTOOLS
#================================
VERSION="1.9"
wget https://github.com/samtools/samtools/releases/download/"$VERSION"/samtools-"$VERSION".tar.bz2
tar xjf samtools-"$VERSION".tar.bz2
rm samtools*.tar.bz2
cd samtools*
./configure
make
make install
cd ..
rm -rf samtools-*
#================================
# INSTALL BWA
#================================
VERSION="0.7.17"
wget https://github.com/lh3/bwa/releases/download/"v"$VERSION/bwa-$VERSION.tar.bz2
tar xf bwa-"$VERSION".tar.bz2
rm bwa-"$VERSION".tar.bz2
cd bwa-*
make
export PATH=$PWD:$PATH
echo "export PATH=$(pwd):$PATH" >> $SINGULARITY_ENVIRONMENT
cd ..
#============================================
# INSTALL PILON
#============================================
wget https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar
echo "alias pilon='java -Xmx16G -jar $PWD/pilon-1.22.jar'" >> $SINGULARITY_ENVIRONMENT
Collection
- Name: rmcolq/Singularity_recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/rmcolq-Singularity_recipes-pilon |
collection name | rmcolq/Singularity_recipes |
branch | master |
tag | pilon |
commit | 2e880b706631e3008de70d428584d22016c62469 |
version (container hash) | 4d378d53510d1d6395119c3cb00af03b |
build date | 2020-04-28T08:53:21.106Z |
size (MB) | 1105 |
size (bytes) | 498290719 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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