TomHarrop/align-utils:salmontools_23eac84
$ singularity pull shub://TomHarrop/align-utils:salmontools_23eac84
Singularity Recipe
Bootstrap: library
From: ubuntu:20.04
%help
Salmon 0.14.1
https://github.com/COMBINE-lab/salmon/releases
%labels
MAINTAINER "Tom Harrop (twharrop@gmail.com)"
VERSION "salmon 0.14.1"
%post
export DEBIAN_FRONTEND=noninteractive
export LC_ALL=C
# set up apt
apt-get clean
rm -r /var/lib/apt/lists/*
apt-get update
apt-get upgrade -y --fix-missing
(
. /etc/os-release
cat << _EOF_ > mirror.txt
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME} main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-security main restricted universe multiverse
_EOF_
mv /etc/apt/sources.list /etc/apt/sources.list.bak
cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
)
apt-get update
apt-get install -y \
build-essential \
bedtools \
cmake \
curl \
git \
language-pack-en \
wget \
zlib1g-dev
# install mashmap
wget -O "mashmap.tar.gz" \
--no-check-certificate \
https://github.com/marbl/MashMap/releases/download/v2.0/mashmap-Linux64-v2.0.tar.gz
mkdir mashmap
tar -zxf mashmap.tar.gz \
-C mashmap \
--strip-components 1
cp mashmap/mashmap /usr/local/bin/
# build salmontools
git clone https://github.com/COMBINE-lab/SalmonTools
cd SalmonTools || exit 1
git checkout 23eac84
chmod -R 755 scripts
mkdir build
cd build || exit 1
cmake ..
make
make install
%environment
export PATH="${PATH}:/SalmonTools/scripts"
%runscript
exec /usr/local/bin/salmontools "$@"
Collection
- Name: TomHarrop/align-utils
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/TomHarrop-align-utils-salmontools_23eac84 |
collection name | TomHarrop/align-utils |
branch | master |
tag | salmontools_23eac84 |
commit | 2b5b9827d1e469b5468ec0a10d67474a9817dea2 |
version (container hash) | 485bd81250128259665ee3c198954204d3a4318d0499dd1090034c692b9aca9e |
build date | 2020-09-29T22:01:57.926Z |
size (MB) | 290.92578125 |
size (bytes) | 305057792 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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