QuentinLetourneur/Let-it-bin:binsanity
$ singularity pull shub://QuentinLetourneur/Let-it-bin:binsanity
Singularity Recipe
Bootstrap: docker
From: ubuntu:16.04
%setup
export LC_ALL=C
%post
mkdir /pasteur
apt -y update
apt -y install wget subread python python-pip camlp4-extra gawk libgsl0-dev libgsl0-dev \
sqlite3 libsqlite3-dev libz-dev m4 ocaml patch ocaml-native-compilers opam zip
pip install biopython scipy scikit-learn pandas
cd /home
wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
tar -xzf hmmer-3.1b2-linux-intel-x86_64.tar.gz
rm hmmer-3.1b2-linux-intel-x86_64.tar.gz
cd hmmer-3.1b2-linux-intel-x86_64
./configure
make
make install
cd easel
make install
cd /home
wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz
tar -xzf v2.6.3.tar.gz
rm v2.6.3.tar.gz
cd Prodigal-2.6.3
make install
cd /home
wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha18/pplacer-linux-v1.1.alpha18-2-gcb55169.zip
unzip pplacer-linux-v1.1.alpha18-2-gcb55169.zip
rm pplacer-linux-v1.1.alpha18-2-gcb55169.zip
cd pplacer-Linux-v1.1.alpha18-2-gcb55169
mv guppy pplacer rppr /usr/local/bin
cd /home
pip install pysam matplotlib dendropy screamingbackpack
wget https://github.com/Ecogenomics/CheckM/archive/v1.0.7.tar.gz
tar -xzf v1.0.7.tar.gz
rm v1.0.7.tar.gz
cd CheckM-1.0.7
python setup.py install
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -xzf checkm_data_2015_01_16.tar.gz
rm checkm_data_2015_01_16.tar.gz
# directly modify the file because cannot be done dynamicly with checkm setRoot
sed -i 's/"dataRoot": ""/"dataRoot": "\/home\/CheckM-1.0.7\/"/' /usr/local/lib/python2.7/dist-packages/checkm/DATA_CONFIG
cd /home
wget https://github.com/edgraham/BinSanity/archive/v0.2.6.1.tar.gz
tar -xzf v0.2.6.1.tar.gz
cd BinSanity-0.2.6.1
sed -i 's/README.rst/README.md/' setup.py
python setup.py install
Collection
- Name: QuentinLetourneur/Let-it-bin
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/QuentinLetourneur-Let-it-bin-binsanity |
collection name | QuentinLetourneur/Let-it-bin |
branch | master |
tag | binsanity |
commit | 647c7b5e55f98b734d8bcb0be2bbc1953b9bb875 |
version (container hash) | d72f799eb63cbe93110b703d0811ddd7 |
build date | 2018-09-02T17:27:42.144Z |
size (MB) | 2878 |
size (bytes) | 854093855 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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