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Benchmarking

pixi run bench-all will download all needed data, and compile parasail.

Prereqs and data

  1. You will need to clone and build parasail
sudo apt-get install libtool
git clone https://github.com/jeffdaily/parasail
cd parasail
autoreconf -fi
./configure
make -j $(nproc)
  1. You will need to have mojo and pixi installed. See the Modular website for install instructions.

Data

  1. Create the benchmarking and data dir
mkdir -p bench/data && cd bench/data
  1. The sequences used for benchmarking are the same as those used in the parasail paper. Query sequences perform the following:
git clone https://github.com/jeffdaily/parasail

The sequences are will be in bench/data/parasail/data.

  1. The reference data can be gotten by:
mkdir refdata && cd refdata
curl https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2015_11/knowledgebase/uniprot_sprot-only2015_11.tar.gz --output uniprot_sprot-only2015_11.tar.gz
tar -xvzf uniprot_sprot-only2015_11.tar.gz