mbhall88/Singularity_recipes:nanoporeqc
$ singularity pull shub://mbhall88/Singularity_recipes:nanoporeqc
Singularity Recipe
Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%help
A container to hold quality control tools and their dependencies for analysing
nanopore data.
Run `singularity exec nanoporeqc.simg` followed by any of the following:
- pistis
- porechop
- filtlong
- minimap2
- samtools
- NanoLyse
- NanoStat
- centrifuge
%environment
PATH=/usr/local/bin:$PATH
%post
# ================================
# INSTALL core dependencies
# ================================
apt-get update
apt-get install -y software-properties-common wget
apt-add-repository universe
apt-get update
apt-get install -y build-essential manpages-dev make zlib1g-dev checkinstall libssl-dev libbz2-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' >> $SINGULARITY_ENVIRONMENT
# ================================
# INSTALL python 3.6
# ================================
PY_VERSION=3.6.4
PY_URL=https://www.python.org/ftp/python/${PY_VERSION}/Python-${PY_VERSION}.tgz
cd /opt
wget "$PY_URL" -O - | tar -xzf -
cd Python-${PY_VERSION}
./configure
make
make install
cd ~
# ================================
# INSTALL latest pistis release (v0.3.3)
# ================================
pip3 install pistis
# ================================
# INSTALL porechop
# ================================
PORECHOP_VERSION=0.2.4
PORECHOP_URL=https://github.com/rrwick/Porechop/archive/v${PORECHOP_VERSION}.tar.gz
apt-get install python3-setuptools python3-pkg-resources
wget "$PORECHOP_URL"
tar xzf v${PORECHOP_VERSION}.tar.gz
rm v${PORECHOP_VERSION}.tar.gz
cd Porechop-${PORECHOP_VERSION}
python3 setup.py install
cd ~
# ================================
# INSTALL filtlong
# ================================
FILTLONG_VERSION=0.2.0
FILTLONG_URL=https://github.com/rrwick/Filtlong/archive/v${FILTLONG_VERSION}.tar.gz
wget "$FILTLONG_URL"
tar xzf v${FILTLONG_VERSION}.tar.gz
rm v${FILTLONG_VERSION}.tar.gz
cd Filtlong-${FILTLONG_VERSION}
make -j
cp bin/filtlong /usr/local/bin
cd ~
# ================================
# INSTALL minimap2
# ================================
MM2_VERSION=2.12
MM2_URL=https://github.com/lh3/minimap2/releases/download/v${MM2_VERSION}/minimap2-${MM2_VERSION}_x64-linux.tar.bz2
wget "$MM2_URL" -O - | tar -jxvf -
cp ./minimap2-${MM2_VERSION}_x64-linux/minimap2 /usr/local/bin
# ================================
# INSTALL samtools
# ================================
SAMTOOLS_VERSION=1.7
SAMTOOLS_URL=https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2
apt-get install -y libncurses5-dev libbz2-dev liblzma-dev
wget "$SAMTOOLS_URL" -O - | tar -jxvf -
cd samtools-${SAMTOOLS_VERSION}
./configure
make
make install
cd ~
# ================================
# INSTALL nanolyse
# ================================
pip3 install NanoLyse
# ================================
# INSTALL nanostats
# ================================
pip3 install nanostat
# ================================
# INSTALL centrifuge
# ================================
apt-get install -y git
# use their github repository as the releases dont seem to be very up to date at the moment
git clone https://github.com/infphilo/centrifuge
cd centrifuge
# go to version 1.0.3-beta
git reset --hard 95178872de36bc10ce83b55397417050eac52e65
make
make install prefix=/usr/local
cd ~
Collection
- Name: mbhall88/Singularity_recipes
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mbhall88-Singularity_recipes-nanoporeqc |
collection name | mbhall88/Singularity_recipes |
branch | master |
tag | nanoporeqc |
commit | 985a10c7fdaf88e538c1ac99fe6fa01c8c0a9814 |
version (container hash) | e310be8fd3b50d5c0c130f8799f8a0ad |
build date | 2020-05-15T06:42:25.398Z |
size (MB) | 1605 |
size (bytes) | 617533471 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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