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install_tools.sh
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install_tools.sh
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##############################
# author [Wankun Deng]
# email [[email protected]]
# create date 2023-02-15 18:35:24
# modify date 2023-02-16 00:24:39
# desc [description]
#############################
# install homer
cd ~
mkdir homer
cd homer
wget http://homer.ucsd.edu/homer/configureHomer.pl
perl configureHomer.pl -install homer
perl configureHomer.pl -install hg19
ln -s /root/homer/bin/findMotifsGenome.pl /usr/local/bin/findMotifsGenome.pl
cd ..
# install kallisto
wget https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz
tar -xzvf kallisto_linux-v0.46.1.tar.gz
cd kallisto
ln -s /root/kallisto/kallisto /usr/local/bin/kallisto
cd ..
# install STAR
wget https://github.com/alexdobin/STAR/archive/2.7.10a.tar.gz
tar -xzf 2.7.10a.tar.gz
cd STAR-2.7.10a/source
make STAR
ln -s /root/STAR-2.7.10a/source/STAR /usr/local/bin/STAR
cd ..
# install cufflinks
wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar -xzf cufflinks-2.2.1.Linux_x86_64.tar.gz
cd cufflinks-2.2.1.Linux_x86_64
rm AUTHORS LICENSE README
cp ./* /usr/local/bin/
cd ..
rm -rf cufflinks-2.2.1.Linux_x86_64
# install bwa
wget https://gigenet.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar -xjvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17
make
cp bwa /usr/local/bin/
cd ..
rm -rf bwa-0.7.17
# ## Modified from https://github.com/hisplan/docker-cellranger, using dropbox to avoid installation of scing
# download_url="https://www.dropbox.com/s/h9mmenub0a7fjun/cellranger-7.1.0.tar"
# version="7.1.0"
# # cell ranger binaries
# wget ${download_url} \
# && tar xf cellranger-${version}.tar \
# && rm -rf cellranger-${version}.tar \
# && mv cellranger-${version} /usr/local/bin/
# ln -s /usr/local/bin/cellranger-${version}/bin/cellranger /usr/local/bin/cellranger
git clone https://github.com/JiekaiLab/scTE.git
cd scTE
python3 setup.py install
cd ..
apt-get update -qq
apt-get install -y libharfbuzz-dev libfribidi-dev
apt-get install -y software-properties-common
add-apt-repository ppa:ubuntugis/ubuntugis-unstable
apt-get update
apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev libsqlite0-dev