maxemil/Biodiversity-pipeline:latest
$ singularity pull shub://maxemil/Biodiversity-pipeline:latest
Singularity Recipe
Bootstrap: docker
From: finalduty/archlinux:daily
%post
######## base system ########
echo "Server = http://mirror.de.leaseweb.net/archlinux/\$repo/os/\$arch" >> /etc/pacman.d/mirrorlist
echo "[lambdait]" >> /etc/pacman.conf
echo "SigLevel = Never" >> /etc/pacman.conf
echo "Server = https://lambda.informatik.uni-tuebingen.de/repo/mypkgs/" >> /etc/pacman.conf
pacman -Syu --noconfirm
pacman -S --noconfirm base-devel \
jdk \
git \
wget \
expect \
tk \
xorg-server-xvfb \
libxtst \
gcc-fortran \
r \
python3 \
python-pip \
python2
######## MEGAN6 ########
cd /usr/local/
wget http://ab.inf.uni-tuebingen.de/data/software/megan6/download/MEGAN_Community_unix_6_8_12.sh
chmod +x MEGAN_Community_unix_6_8_12.sh
./MEGAN_Community_unix_6_8_12.sh -q
cd megan
wget http://ab.inf.uni-tuebingen.de/data/software/megan6/download/nucl_acc2tax-May2017.abin.zip
unzip nucl_acc2tax-May2017.abin.zip
cd ..
######## MALT ########
wget http://ab.inf.uni-tuebingen.de/data/software/malt/download/MALT_unix_0_3_9.sh
chmod +x MALT_unix_0_3_9.sh
./MALT_unix_0_3_9.sh -q
######## python ########
pip install biopython pandas numpy requests scipy ete3
######## FUNGuild ########
cd /usr/local
git clone https://github.com/UMNFuN/FUNGuild.git
ln /usr/local/FUNGuild/Guilds_v1.1.py /usr/local/bin/
######## Vsearch ########
wget https://github.com/torognes/vsearch/archive/v2.4.3.tar.gz
tar xzf v2.4.3.tar.gz
cd vsearch-2.4.3
./autogen.sh
./configure
make
make install
######## R ########
wget https://cran.r-project.org/src/contrib/picante_1.6-2.tar.gz
wget https://cran.r-project.org/src/contrib/vegan_2.4-5.tar.gz
wget https://cran.r-project.org/src/contrib/permute_0.9-4.tar.gz
wget https://cran.r-project.org/src/contrib/ape_5.0.tar.gz
wget https://cran.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz
wget https://cran.r-project.org/src/contrib/futile.options_1.0.0.tar.gz
wget https://cran.r-project.org/src/contrib/lambda.r_1.2.tar.gz
wget https://cran.r-project.org/src/contrib/VennDiagram_1.6.18.tar.gz
wget https://cran.r-project.org/src/contrib/Rcpp_0.12.14.tar.gz
R CMD INSTALL permute_0.9-4.tar.gz \
Rcpp_0.12.14.tar.gz \
ape_5.0.tar.gz \
vegan_2.4-5.tar.gz \
picante_1.6-2.tar.gz \
lambda.r_1.2.tar.gz \
futile.options_1.0.0.tar.gz \
futile.logger_1.4.3.tar.gz \
VennDiagram_1.6.18.tar.gz
%files
binaries/spaced /usr/local/bin/spaced
%test
/usr/local/malt/malt-build -h
/usr/local/malt/malt-run -h
/usr/local/megan/tools/rma2info -h
vsearch --version
python3 /usr/local/bin/Guilds_v1.1.py -h
%labels
Maintainer max-emil.schon@icm.uu.se
Collection
- Name: maxemil/Biodiversity-pipeline
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/maxemil-Biodiversity-pipeline-latest |
collection name | maxemil/Biodiversity-pipeline |
branch | master |
tag | latest |
commit | 8dc5f10809cfd12dc30b904d0e81f5abf36d9616 |
version (container hash) | dd9060cbeabadf2ac7917b3cffd47338 |
build date | 2020-03-27T12:15:22.763Z |
size (MB) | 5695 |
size (bytes) | 3474735135 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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