Hello everyone,
since I found a little bit challenging to collect all the pieces to have PhyloSift working, I’m sharing here some notes, should they be useful for somebody…
In particular, it’s currently not possible to automatically download the markers database as the hard-coded URLs are no longer working.
The most updated website is https://phylosift.wordpress.com/. I installed both the package and the markers database in the same directory, totally accounting for ~7 Gb after cleaning up the archives.
# Download package
git clone https://github.com/gjospin/PhyloSift.git
# Download markers (here in a ./markers subdirectory)
mkdir markers
wget -O markers/data.zip https://ndownloader.figshare.com/articles/5755404/versions/4
# Expand the archives
cd markers
tar xvfz markers_20140913.tgz
mv markers markers_20140913
tar xvfz ncbi.tgz
tar xvfz markers.tgz
# Copy the configuration file template to your home
cp ./PhyloSift/phylosiftrc ~/.phylosiftrc
# Install required Perl modules
for MOD in "App::Cmd::Setup" "File::NFSLock" "Bio::Phylo" JSON;
do
perl -M${MOD} -e 1 2>/dev/null;
if [[ $? -gt 0 ]]; then
echo "Attempting installation of $MOD"
cpanm -i $MOD
fi
done
Finally, we need to edit our ~/.phylosiftrc to point to the correct markers directory. You need to edit the following lines adding the full paths to the markers directory without any trailing slash:
$marker_path="${INSTALL_DIR}/markers/markers";
$ncbi_path="${INSTALL_DIR}/markers/ncbi";
$marker_dir="${INSTALL_DIR}/markers/markers";
$markers_extended_dir="${INSTALL_DIR}/markers/markers_20140913";
$ncbi_dir = "${INSTALL_DIR}/markers/markers";