mbhall88/Singularity_recipes:krakenuniq
$ singularity pull shub://mbhall88/Singularity_recipes:krakenuniq
Singularity Recipe
Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%post
apt update
apt install -y software-properties-common
apt-add-repository universe
apt update
apt install -y git wget build-essential
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' >> $SINGULARITY_ENVIRONMENT
echo "export PATH=/usr/local:/usr/local/bin:$PATH" >> $SINGULARITY_ENVIRONMENT
# ================================
# INSTALL blast tools (dustmasker req. for kraken)
# ================================
apt install -y libidn11-dev
VERSION="2.7.1"
URL=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"$VERSION"/ncbi-blast-"$VERSION"+-x64-linux.tar.gz
wget -O - "$URL" | tar xzf -
cp ncbi*/bin/dustmasker /usr/local/bin/
rm -rf ncbi-blast*
cd ~
# ================================
# INSTALL jellyfish
# ================================
VERSION="1.1.11"
URL=http://www.cbcb.umd.edu/software/jellyfish/jellyfish-"$VERSION".tar.gz
wget -O - "$URL" | tar xzf -
cd jellyfish*
./configure --prefix=/usr/local/
make
make install
# ================================
# INSTALL krakenuniq
# ================================
VERSION="0.5.7"
URL=https://github.com/fbreitwieser/krakenuniq/archive/v"$VERSION".tar.gz
apt install -y zlib1g-dev
wget -O - "$URL" | tar xzf -
cd krakenuniq-"$VERSION"
echo "export PATH=$(pwd):$PATH" >> $SINGULARITY_ENVIRONMENT
./install_krakenuniq.sh -j $(pwd)
cd ~
perl -MCPAN -e'install "LWP::Simple"'
ln -s /krakenuniq-"$VERSION"/krakenuniq /krakenuniq-"$VERSION"/krakenuniq-build /krakenuniq-"$VERSION"/krakenuniq-download /krakenuniq-"$VERSION"/krakenuniq-extract-reads /krakenuniq-"$VERSION"/krakenuniq-filter /krakenuniq-"$VERSION"/krakenuniq-mpa-report /krakenuniq-"$VERSION"/krakenuniq-report /krakenuniq-"$VERSION"/krakenuniq-translate /usr/local/bin/
Collection
- Name: mbhall88/Singularity_recipes
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mbhall88-Singularity_recipes-krakenuniq |
collection name | mbhall88/Singularity_recipes |
branch | master |
tag | krakenuniq |
commit | d76b3062b0eb29334c26e9e614e708c6cedf27d7 |
version (container hash) | c9cacb07202e873d68f324837c8baa01 |
build date | 2019-01-09T15:39:53.455Z |
size (MB) | 760 |
size (bytes) | 260857887 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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