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DIVIA.def
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DIVIA.def
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BootStrap: docker
From: ubuntu:latest
%apprun Rscript
exec Rscript "${@}"
%post
# apt-get update
# apt-get install -y unzip
# apt-get install -y git
# Install python2
apt-get update && \
apt-get install -y python2 python2-minimal dh-python
cd /usr/bin/ && \
ln -s python2 python &&
cd ~
# apt-get install -y python python-dev python-numpy python-biopython python-xlrd python-openpyxl
## Install R
export R_VERSION=4.2.2
echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
# Get dependencies
apt --fix-broken install
apt-get update
apt-get upgrade -y
apt-get install -y --no-install-recommends \
locales
# Configure default locale
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
locale-gen en_US.utf8
/usr/sbin/update-locale LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
##install perl module
apt-get install -y cmake unzip bzip2 tar gzip pigz
## cpan App::cpanminus && \
## cpan install DB_File URI::Escape Set::IntervalTree Carp::Assert JSON::XS PerlIO::gzip
## apt-get -y install cpanminus && \
## cpan install JSON::XS URI::Escape Carp::Assert
## cpan install PerlIO::gzip && \
##cpanm --force install Carp::Assert && \
## cpan install Set::IntervalTree && \
## cpanm --force install URI::Escape
## cpan install DB_File
apt-get update --fix-missing
apt-get install -y --no-install-recommends \
software-properties-common \
dirmngr \
wget \
apt-utils
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository \
"deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt-get install -y --no-install-recommends \
r-base=${R_VERSION}*
apt-get install -y --no-install-recommends \
r-base-core=${R_VERSION}*
apt-get install -y --no-install-recommends \
r-base-dev=${R_VERSION}*
apt-get install -y --no-install-recommends \
r-base-html=${R_VERSION}*
apt-get install -y --no-install-recommends \
r-doc-html=${R_VERSION}*
apt-get install -y --no-install-recommends \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libcairo2-dev \
libxt-dev \
libopenblas-dev \
python3 \
python3-pip \
nano \
vim \
git \
curl
apt-get install -y\
libharfbuzz-dev \
libfribidi-dev
apt-get install -y libfreetype6-dev
apt-get install -y libpng-dev
apt-get install -y libtiff5-dev
apt-get install -y libjpeg-dev
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
# Add a directory for host R libraries
mkdir -p /library
echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site
mkdir tools
wget -qO tools/quarto-1.2.94-linux-amd64.deb https://github.com/quarto-dev/quarto-cli/releases/download/v1.2.94/quarto-1.2.94-linux-amd64.deb
dpkg -i tools/quarto-1.2.94-linux-amd64.deb
quarto tools install tinytex
quarto tools install chromium
# Now that we have all the required package, update to the github version
git clone https://github.com/quarto-dev/quarto-cli
cd quarto-cli
./configure.sh
cd ~
#Install needed R packages
R --slave -e 'install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")'
R --slave -e 'install.packages("BiocManager")'
EXP="pak::pkg_install(c('devtools','ranger','multiclassPairs','mclust','preprocessCore','DESeq2','patchwork','pheatmap','switchBox','Rtsne','GGally','limma','ggrepel','cli','logger','openxlsx','fs','funr','readxl','readr','glue','tidyverse', 'rtracklayer','argparse','ggplot2','ggsci','formattable','circlize', 'kableExtra','logger','bookdown','bs4Dash', 'gt','pingr','trackViewer','csaw','tryCatchLog','reshape2','genomation','pander', 'BSgenome.Mmusculus.UCSC.mm10','BSgenome.Hsapiens.UCSC.hg38','TxDb.Mmusculus.UCSC.mm9.knownGene', 'TxDb.Mmusculus.UCSC.mm10.knownGene','org.Mm.eg.db','TxDb.Hsapiens.UCSC.hg19.knownGene','TxDb.Hsapiens.UCSC.hg38.knownGene', 'org.Hs.eg.db','TxDb.Scerevisiae.UCSC.sacCer3.sgdGene', 'org.Sc.sgd.db'))"
# EXP="pak::pkg_install(c('devtools','cli','logger','openxlsx','fs','funr','readxl','readr','glue','tidyverse', 'rtracklayer','argparse','ggplot2','ggsci','formattable','circlize', 'kableExtra','logger','bookdown','bs4Dash','gt','pingr','trackViewer','csaw','tryCatchLog','reshape2','genomation','pander'))"
R -e "$EXP"
R --slave -e 'devtools::install_github("sirusb/kableExtra")'
Rscript -e 'devtools::install_github(repo = "honzee/RNAseqCNV")'
# Install python packages
pip install matplotlib plotly_express click pandas rich seaborn scikit-learn openpyxl xlsxwriter xlrd jupyter jupyterlab jupyter-cache
## autoheaders
pip3 install autoheaders
## g++ JAVA zlib
apt-get update && \
apt-get install -y build-essential openjdk-8-jdk
## autoconfig
apt-get install -y automake autotools-dev libsigsegv2 m4
apt-get install -y autoconf
# Clean up
# rm -rf /var/lib/apt/lists/*
# rm -rf /tmp/Rtmp*
echo "unset XDG_RUNTIME_DIR" >> ~/.bashrc
# apt-get install -y cmake unzip bzip2 tar gzip pigz
## htslib
cd /usr/local && \
git clone --recurse-submodules https://github.com/samtools/htslib.git && \
cd htslib && \
autoreconf -i && \
./configure && make && make install
## samtools
cd /usr/local && \
git clone --recurse-submodules https://github.com/samtools/samtools.git && \
cd samtools && \
autoheader && \
autoconf -Wno-syntax && \
./configure && make && make install
## install tabix
cd /usr/local/ &&
wget --no-check-certificate https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2 && tar jxvf tabix-0.2.6.tar.bz2 && cd tabix-0.2.6 && make && cp bgzip tabix /usr/local/bin/ && rm /usr/local/tabix-0.2.6.tar.bz2
## install cutadapt
python3 -m pip install cutadapt
## trim_galore
cd /usr/local && \
wget -q https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.tar.gz -O trim_galore.tar.gz && \
tar xzf trim_galore.tar.gz && \
ln -s /usr/local/TrimGalore-0.6.6/trim_galore /usr/local/bin/trim_galore && \
rm trim_galore.tar.gz
## fastqc
cd /usr/local && \
wget -q https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip && \
unzip fastqc_v0.11.9.zip && \
chmod 775 /usr/local/FastQC/fastqc && \
ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc && \
rm fastqc_v0.11.9.zip
## gatk-4.1.8
cd /usr/local && \
wget -q https://github.com/broadinstitute/gatk/releases/download/4.1.8.0/gatk-4.1.8.0.zip && \
unzip gatk-4.1.8.0.zip && \
ln -s /usr/local/gatk-4.1.8.0/gatk /usr/local/bin/gatk && \
rm gatk-4.1.8.0.zip
## STAR-2.7.9a
cd /usr/local && \
wget -q https://github.com/alexdobin/STAR/archive/refs/tags/2.7.9a.tar.gz -O star.tar.gz && \
tar xzf star.tar.gz && \
cd STAR-2.7.9a/source && \
make STAR && \
cp STAR /usr/local/bin && \
rm /usr/local/star.tar.gz
## RSEM
cd /usr/local && \
wget https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz && \
tar xzf v1.3.3.tar.gz && \
cd RSEM-1.3.3 && \
make && make install
## arriba-2.3.0
cd /usr/local && \
wget -q https://github.com/suhrig/arriba/releases/download/v2.3.0/arriba_v2.3.0.tar.gz && \
tar -xzf arriba_v2.3.0.tar.gz && \
cd arriba_v2.3.0 && \
make && \
rm /usr/local/arriba_v2.3.0.tar.gz
## Install perl modules for STAR-Fusion
apt-get -y install cpanminus && \
cpan install JSON::XS URI::Escape Carp::Assert
## STAR-Fusion
cd /usr/local && \
wget -q https://github.com/STAR-Fusion/STAR-Fusion/releases/download/v1.6.0/STAR-Fusion-v1.6.0.FULL.tar.gz && \
tar -xzf STAR-Fusion-v1.6.0.FULL.tar.gz && \
cd STAR-Fusion-v1.6.0 && \
make && \
rm /usr/local/STAR-Fusion-v1.6.0.FULL.tar.gz
# install STAR-Fusion v1.11.1
## git clone --recursive https://github.com/STAR-Fusion/STAR-Fusion.git && \
## cd STAR-Fusion && \
## make
%runscript
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this text code will run whenever the container
# is called as an executable or with `singularity run`
%environment
export LC_ALL=C
export R_LIBS=/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
export PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion-v1.6.0:/usr/local/usr/local/RSEM-1.3.3:$PATH
# export PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/usr/local/RSEM-1.3.3:$PATH