CellFishing
I tried to use CellFishing written in Julia. It was my first time to use Julia, so I started from the installation of Julia with Homebrew.
# Install Julia
brew cask install julia
# Install CellFishing
julia -e 'using Pkg; Pkg.add(PackageSpec(url="git://github.com/bicycle1885/CellFishing.jl.git"))'
# Run test for CellFishing
julia -e 'using Pkg; Pkg.test("CellFishing")'
# git clone CellFishing
git clone https://github.com/bicycle1885/CellFishing.jl
After installing julia, I followed the instruction in CellFishing website, but the test code was failed.
According to CellFishing developer, the reason for that failure was that zstd was missing. So I installed zstd.
# Install zstd via Homebrew
brew install -v zstd
And I tried command-line interface for CellFishing.
Some packages (HDF5 and DocOpt) were requred to run cellfishing build command.
# Install required packages in julia
julia -e 'using Pkg; Pkg.add("HDF5")'
julia -e 'using Pkg; Pkg.add("DocOpt")'
Of course, data for the search was required. It could be downloaded from http://bimsbstatic.mdc-berlin.de/rajewsky/PSCA/all_sgete_4GU75.loom.gz liked from Planaria Single Cell Atlas website.
# Getting data for the search
curl -O http://bimsbstatic.mdc-berlin.de/rajewsky/PSCA/all_sgete_4GU75.loom.gz
gzip -dc all_sgete_4GU75.loom.gz > Plass2018.dge.loom
After getting the file, I successfully ran the code!
# Run CellFishing
./bin/cellfishing build Plass2018.dge.loom
./bin/cellfishing search Plass2018.dge.loom.cf Plass2018.dge.loom >neighbors.tsv