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@meren meren/anvio-arch-setup.sh
Last active Jun 26, 2016

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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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