sequana/sequana:0_6_2
$ singularity pull shub://sequana/sequana:0_6_2
Singularity Recipe
#BootStrap: debootstrap
#DistType "debian"
#MirrorURL: http://us.archive.ubuntu.com/ubuntu/
#OSVersion: xenial
BootStrap: docker
From: ubuntu:16.04
%labels
AUTHOR Thomas Cokelaer
%post
apt-get update
apt-get install -y wget
apt-get install -y bzip2
apt-get install -y vim
apt-get install -y libgl1-mesa-glx # will be required by pyqt
apt-get install -y fontconfig # for sequanix/qt fonts otherwise no text in menus
# for fastqc
apt-get install -y libxrender1
apt-get install -y libxtst6
apt-get install -y libxi6
# for sequanix (Qt plugin) otherwise libxcb missing
apt-get install -y libsm-dev
apt-get install -y libxcomposite-dev
# This is a large data set again. When using the container a sroot, sequanix
# looks good but in normal mode, the menu is blank...and this seems to solve
# the issue
apt-get install -y libgnomeui-0
# install anaconda
if [ ! -d /usr/local/anaconda ]; then
#wget https://repo.continuum.io/miniconda/Miniconda3-4.3.14-Linux-x86_64.sh\
# for now, we use 4.2.12 to have python3.5 by default so no need to
# create a new env saving space in the process. The reason for using 3.5
# is inherent to the packages used at the moment.
wget https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh\
-O ~/anaconda.sh && \
bash ~/anaconda.sh -b -p /usr/local/anaconda && \
rm ~/anaconda.sh
fi
# set anaconda path
export PATH=$PATH:/usr/local/anaconda/bin
conda update conda
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
# The main packages for sequana:
conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements.txt
# equivalent to requirements_pipelines.txt version 0.6.2
conda install --file https://raw.githubusercontent.com/sequana/sequana/master/requirements_pipelines.txt
# Let us save some space
conda clean --packages -y
# For the pipelines_extra, busco takes for ever, so we skip it for now
conda install -y canu
# this one hangs for ever busco==3.0.2
# conda install -y prokka # takes lots of place
# Let us save some space
conda clean --packages -y
# Sequana source code
pip install sequana==0.6.2
conda clean --all -y # next requires lots of space
rm -rf /usr/local/anaconda/pkgs
# pysam/bzip/hstlib is tricky. We pin versions as follows
conda install --override-channels -c conda-forge bzip2
conda install --override-channels -c bioconda -c conda-forge htslib==1.5.0
conda install pysam==0.12.0.1
if [ ! -d /data ]; then mkdir /data; fi
if [ ! -d /scripts ]; then mkdir /scripts; fi
if [ ! -d /scratch ]; then mkdir /scratch; fi
if [ ! -d /mounting ]; then mkdir /mounting; fi
if [ ! -d /pasteur ]; then mkdir /pasteur; fi
echo "backend:tkagg" > matplotlibrc
export PATH=$PATH:/usr/local/anaconda/bin
export LANG=C # prevents perl for raising warnings
export PERL5LIB=/usr/local/anaconda/lib/perl5/5.22.0
python -c "import sequana" # creates config file and check installation
%environment
export PATH=$PATH:/usr/local/anaconda/bin
export LANG=C # prevents perl for raising warnings
export PERL5LIB=/usr/local/anaconda/lib/perl5/5.22.0
#echo "backend:agg" > matplotlibrc
Collection
- Name: sequana/sequana
- License: BSD 3-Clause “New” or “Revised” License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/sequana-sequana-0_6_2 |
collection name | sequana/sequana |
branch | master |
tag | 0_6_2 |
commit | 98a45ee688c8788852ffe7daff826885bd4362d7 |
version (container hash) | 1f91ad666cf0776f8afd3b200aafe902 |
build date | 2018-01-08T16:00:18.550Z |
size (MB) | 4714 |
size (bytes) | 1419460639 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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