BootStrap: docker
From: centos:8

%help
This is a singularity container packing the Bionano Solve pipeline in version 3.6.1 and all the dedicated environnement set up for proper usage of the pipeline
Author : yannis.duffourd@u-bourgogne.fr
Bionano Solve pipeline is the property of Bionano Genomics Inc. All Rights Reserved
This singularity recipe is open source and free. Please redistribute it as well.
No warranty is provided.
Bionano tools are installed in /home/bionano/tools/
R & Rscript are installed in /opt/bionano/bin
python3.7 is installed in /opt/bionano/bin
python3.7 libs are in /opt/bionano/lib/python3.7:/opt/bionano/lib/python3.7/site-packages/
Launching a complete assembly could be perform with this command :
singularity exec -e -w bionano_solve_3.7.sif \
python3.7 /home/bionano/tools/pipeline/1.0/Pipeline/1.0/pipelineCL.py \
-b <inputfile> \
-r <path to digested reference> \
-l <path to output dir> \
-t /home/bionano/tools/pipeline/1.0/RefAligner/1.0/ \
--species-reference human_hg19 \
-N 4 -f 0.2 -y \
-a /home/bionano/tools/pipeline/1.0/RefAligner/1.0/optArguments_haplotype_saphyr_human.xml \
--autoRestart \
-T <nb threads>

%setup
mkdir ${SINGULARITY_ROOTFS}/data

%files
  /data/bionano/3.6.1/access.tools.tgz /home/bionano/access.tools.tgz

%post
sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*

yum update -y
yum install -y epel-release


BASHRC=/home/bionano/.bashrc
# echo "export DRMAA_LIBRARY_PATH=/home/sge/lib/lx-amd64/libdrmaa.so" >> $BASHRC
echo "export OMP_WAIT_POLICY=PASSIVE" >> $BASHRC
echo "export PATH=/opt/bionano/bin:\$PATH" >> $BASHRC

# system libs
yum groupinstall -y development
yum --enablerepo=powertools install -y libyaml-devel libffi-devel
yum install -y wget which time zlib-devel munge-libs jemalloc openssl-devel sqlite-devel bzip2-devel xz-libs libcurl-devel libtiff-devel libjpeg-devel libxml2-devel libffi-devel.x86_64 libyaml-devel dos2unix perl-CPAN gcc perl-App-cpanminus perl-Config-Tiny expat-devel python3-lit llvm-devel llvm-toolset gcc-gfortran readline-devel libX11-devel libXt-devel xorg-x11-server-utils xorg-x11-server-Xorg  xorg-x11-xauth pcre pcre-devel

mkdir /opt/bionano/
mkdir /opt/bionano/src
mkdir /opt/bionano/bin
mkdir /opt/bionano/lib

# install R 3.6.0
cd /opt/bionano/src/
wget https://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz
tar -xzvf R-3.6.0.tar.gz
cd R-3.6.0
./configure --prefix=/opt/bionano/
make -j 8
make install

# perl modules
cpanm JSON JSON::XS XML::Parser && cpanm PerlIO::Util --force && cpanm threads --force && cpanm XML::SAX --force && cpanm Config::Simple File::Path File::Slurp File::Copy File::Copy::Recursive Scalar::Util Data::Dumper XML::Simple DateTime DateTime::Format::Human::Duration IO::Select File::Spec List::MoreUtils


# install bionano solve
cd /home/bionano
tar -xzvf access.tools.tgz

# install python3
cd /opt/bionano/src/
wget https://www.python.org/ftp/python/3.7.7/Python-3.7.7.tar.xz
xz -d Python-3.7.7.tar.xz
tar -xvf Python-3.7.7.tar
cd Python-3.7.7
./configure --prefix=/opt/bionano/
make -j 8
make altinstall


# update pip
/opt/bionano/bin/python3.7 -m pip install --upgrade pip

# python3.7 packages
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages lxml==4.5.0
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pandas==1.0.3
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages natsort==7.0.1
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages drmaa==0.7.9
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages numpy==1.18.4
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages llvmlite
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages numba==0.42.0
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pandasql==0.7.3
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages scikit-learn==0.22.1
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pyyaml==5.3.1
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages intervaltree==3.0.2
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages scipy==1.4.1
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages imbalanced-learn==0.6.2
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages matplotlib==3.1.3
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages lightgbm==2.3.0
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages xlrd==1.2.0
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pytest==5.4.2
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pytest-forked
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pytest-xdist
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages pytest-cov
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages coverage==5.4
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages hmmlearn
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages xgboost==0.90
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages joblib==0.13.2
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages xlrd
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages wheel
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/pyBionano
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/SVConfModels
/opt/bionano/bin/python3.7 -m pip install --upgrade -t /opt/bionano/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/lohdetection

# install bng from bionano
# /opt/bionano/bin/python3.7 /home/bionano/tools/access/1.0/bng-install all

# R packages
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=digest&version=0.6.13", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=magrittr&version=1.5", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=assertthat&version=0.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=prettyunits&version=1.0.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bit&version=1.1-13", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=DBI&version=0.8", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=memoise&version=1.1.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pkgconfig&version=2.0.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=Rcpp&version=1.0.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=BH&version=1.66.0-1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=plogr&version=0.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=crayon&version=1.3.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=cli&version=1.0.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=praise&version=1.0.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R6&version=2.3.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=rlang&version=0.1.6", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=withr&version=2.1.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=testthat&version=2.0.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.methodsS3&version=1.7.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.oo&version=1.22.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=R.utils&version=2.8.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=data.table&version=1.12.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=outliers&version=0.14", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=diptest&version=0.75-7", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=intervals&version=0.15.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=fansi&version=0.3.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=utf8&version=1.1.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pillar&version=1.0.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=colorspace&version=1.3-2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=labeling&version=0.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=munsell&version=0.5.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=RColorBrewer&version=1.0-5", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=viridisLite&version=0.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=glue&version=1.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=stringi&version=1.1.6", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=plyr&version=1.8.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=stringr&version=1.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=lattice&version=0.20-35", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=nlme&version=3.1-131", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=Matrix&version=1.2-15", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=gtable&version=0.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=lazyeval&version=0.2.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=MASS&version=7.3-29", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=mgcv&version=1.7-28", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=reshape2&version=1.4.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=dichromat&version=2.0-0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=scales&version=0.5.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tibble&version=1.4.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=ggplot2&version=2.2.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=purrr&version=0.2.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tidyselect&version=0.2.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bindr&version=0.1.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=bindrcpp&version=0.2.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=dplyr&version=0.7.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=RSQLite&version=0.11.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=XML&version=3.98-1.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tiff&version=0.1-5", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=inline&version=0.3.13", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=igraph&version=1.2.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=wbs&version=1.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=argparser&version=0.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=htmltools&version=0.3.6", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=jsonlite&version=1.6", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=yaml&version=2.2.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=htmlwidgets&version=1.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=maps&version=3.3.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=hexbin&version=1.27.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=pryr&version=0.1.4", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=curl&version=3.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=mime&version=0.6", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=sys&version=3.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=askpass&version=1.1", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=openssl&version=1.3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=httr&version=1.4.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=evaluate&version=0.13", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=highr&version=0.8", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=markdown&version=0.9", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=xfun&version=0.6", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=knitr&version=1.22", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=base64enc&version=0.1-3", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=tinytex&version=0.12", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=rmarkdown&version=1.12", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=gistr&version=0.4.2", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("https://cran.r-project.org/package=rbokeh&version=0.5.0", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("/home/bionano/tools/pipeline/1.0/bionano_packages/BionanoR", repos=NULL, type="source")'
/opt/bionano/bin/Rscript -e 'install.packages("/home/bionano/tools/pipeline/1.0/bionano_packages/FractCNV", repos=NULL, type="source")'

# cleanup
rm /home/bionano/access.tools.tgz

%labels
Maintainer Yannis Duffourd
Updater Yannis Duffourd <yannis.duffourd@u-bourgogne.fr>
ContainerVersion v0.1
Software bionano solve pipeline v3.6.1

%environment
    export PATH=/opt/bionano/bin:/usr/ccub/sge-8.1.8/bin:/usr/ccub/sge-8.1.8/bin/lx-amd64:$PATH
    export PYTHON_PATH=/opt/bionano/lib/python3.7:/opt/bionano/lib/python3.7/site-packages/
    export PYTHON=/opt/bionano/bin/python3.7
    export DRMAA_LIBRARY_PATH=/usr/ccub/sge-8.1.8/lib/lx-amd64/libdrmaa.so




%runscript
echo "OK"