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Commit 771636ea authored by Yannis Duffourd's avatar Yannis Duffourd
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Changing all path to original bionano installation path

parent 0aa234b9
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bionano_solve_3.7.def
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......@@ -8,9 +8,9 @@ Bionano Solve pipeline is the property of Bionano Genomics Inc. All Rights Reser
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/
R & Rscript are installed in /usr/local/bin
python3.7 is installed in /usr/local/bin
python3.7 libs are in /usr/local/lib/python3.7:/usr/local/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 \
......@@ -35,15 +35,11 @@ yum update -y
yum install -y epel-release
mkdir /home/bionano
mkdir /opt/bionano/
mkdir /opt/bionano/src
mkdir /opt/bionano/bin
mkdir /opt/bionano/lib
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
echo "export PATH=/usr/local/bin:\$PATH" >> $BASHRC
# system libs
yum groupinstall -y development
......@@ -51,11 +47,11 @@ 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
# install R 3.6.0
cd /opt/bionano/src/
cd /usr/local/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/
./configure --prefix=/usr/local/
make -j 8
make install
......@@ -68,139 +64,136 @@ wget -N www.bnxinstall.com/access/tools/access.tools.tgz
tar -xzvf access.tools.tgz
# install python3
cd /opt/bionano/src/
cd /usr/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/
./configure --prefix=/usr/local
make -j 8
make altinstall
# update pip
/opt/bionano/bin/python3.7 -m pip install --upgrade pip
/usr/local/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 /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
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages lxml==4.5.0
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pandas==1.0.3
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages natsort==7.0.1
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages drmaa==0.7.9
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages numpy==1.18.4
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages llvmlite
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages numba==0.42.0
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pandasql==0.7.3
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages scikit-learn==0.22.1
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pyyaml==5.3.1
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages intervaltree==3.0.2
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages scipy==1.4.1
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages imbalanced-learn==0.6.2
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages matplotlib==3.1.3
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages lightgbm==2.3.0
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages xlrd==1.2.0
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pytest==5.4.2
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pytest-forked
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pytest-xdist
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages pytest-cov
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages coverage==5.4
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages hmmlearn
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages xgboost==0.90
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages joblib==0.13.2
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages xlrd
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/pyBionano
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/SVConfModels
/usr/local/bin/python3.7 -m pip install --upgrade -t /usr/local/lib/python3.7/site-packages /home/bionano/tools/pipeline/1.0/bionano_packages/lohdetection
# 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")'
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%labels
Maintainer Yannis Duffourd
......@@ -209,9 +202,9 @@ ContainerVersion v0.1
Software bionano solve pipeline v3.7.1
%environment
export PATH=/opt/bionano/bin:$PATH
export PYTHON_PATH=/opt/bionano/lib/python3.7:/opt/bionano/lib/python3.7/site-packages/
export PYTHON=/opt/bionano/bin/python3.7
export PATH=/usr/local/bin:$PATH
export PYTHON_PATH=/usr/local/lib/python3.7:/usr/local/lib/python3.7/site-packages/
export PYTHON=/usr/local/bin/python3.7
......
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