Anvi'o installer for Arch Linux by Canberk Koç & Çağrı Ulaş
#!/bin/bash | |
set -e | |
# Get fresh repo | |
sudo pacman -Syy | |
# Using aur for some packages so get some yaourt | |
sudo pacman -S --noconfirm yajl | |
# Creating workbench | |
mkdir -pv /tmp/yaourt/{package-query_pkgbuild,yaourt_pkgbuild} | |
# Getting pkgbuilds | |
curl 'https://aur.archlinux.org/cgit/aur.git/plain/PKGBUILD?h=package-query' > /tmp/yaourt/package-query_pkgbuild/PKGBUILD | |
curl 'https://aur.archlinux.org/cgit/aur.git/plain/PKGBUILD?h=yaourt' > /tmp/yaourt/yaourt_pkgbuild/PKGBUILD | |
cd /tmp/yaourt/package-query_pkgbuild/ | |
makepkg -i --noconfirm | |
cd /tmp/yaourt/yaourt_pkgbuild | |
makepkg -i --noconfirm | |
yaourt -S --noconfirm wget | |
#Libraries | |
yaourt -S --noconfirm gsl\ | |
hdf5 | |
#Python | |
yaourt -S --noconfirm python2-numpy\ | |
cython2\ | |
python2-pip\ | |
zlib\ | |
sqlite\ | |
python2-scipy\ | |
python2-scikit-learn\ | |
python2-bottle\ | |
python2-h5py | |
#Fortran | |
yaourt -S --noconfirm blas\ | |
lapack | |
#C | |
yaourt -S --noconfirm cblas | |
#Pip Execution | |
sudo pip2 install ete2>=2.2 | |
# prodigal | |
wget https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz | |
tar -zxvf v2.6.2.tar.gz && cd Prodigal-2.6.2/ && make | |
sudo cp prodigal /usr/bin/ | |
cd | |
rm -rf v2.6.2.tar.gz Prodigal-2.6.2 | |
# hmmer | |
yaourt -S --noconfirm hmmer | |
# Installing | |
sudo pip2 install anvio |
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