Download ASAFind to install locally

For local installation, a command line version of ASAFind can be downloaded from our GitHub repository:

https://github.com/ASAFind/ASAFind-2

Installation steps

Using the GiHub function, you can either dowload the files as a zip archive, or you can clone the repository using the provided URL. After download of the latest version, follow these installation steps:

• step into the directory where you want to make the installation e.g.
  cd /home/marta/asafind
• make the installation directory here eg.
  mkdir asafind_line_command
• step into this directory
  cd asafind_line_command
• unpack the installation package asafind_line_command.zip
  unzip -a asafind_line_command.zip
• run the following three commands from the command line
  python3 -m venv asafind_line_command
  . asafind_line_command/bin/activate
  pip install --upgrade pip
  pip install -r requirements.txt
  

It will create the environment called asafind_line_command including subdirectries temp and output, install all required packages activate it.
python S1_ASAFind_v3.py --help

usage: S1_ASAFind_v3.py

[-h] -f FASTA_FILE [-p SIGNALP_FILE] [-s SIMPLE_SCORE_CUTOFF] [-t SCORE_TABLE_FILE] [-o OUT_FILE] [-w] [-v1] [-ppc] [-s_ppc SCORE_CUTOFF_PPC] [-t_ppc SCORE_TABLE_FILE_PPC] [-l {yes,no}] -my_org MY_ORGANISM [-v]