Initialization - Kinggerm/GetOrganelle GitHub Wiki

Default directory

The initialized database will be located at ~/.GetOrganelle by default. It can be changed by using the command line parameter --config-dir for a single run, or by using the shell environment variable GETORG_PATH for the entire running environment.

For example, one may change the default database directory into /home/shared/.GetOrganelle by adding

GETORG_PATH=/home/shared/.GetOrganelle export GETORG_PATH

to /etc/profile for system-wide usage, or to ~/.bashrc for user-wide usage in Ubuntu Desktop, or to ~/.bash_profile for user-wide usage in bash, or to ~/.zshrc for user-wide usage in Zsh

and restarting the shell before initialization.

Option 1 Initialization from Github

By default, get_organelle_config.py will automatically access this repository to download and build the SeedDatabase and LabelDatabase of the latest version. e.g.

get_organelle_config.py -a fungus_mt

Due to the unstable accessibility to Github in some regions, the get_organelle_config.py sometimes fails with connection error (e.g. timeout). In most cases, try the above command for more times will simply work.

Option 2 Initialization from local files

If Initialization from Github still fails after many trials, download this repository and run get_organelle_config.py with the flag --use-local. Making your own database is feasible if you use the same directory structure, but not recommended.

Supposing you want to install version 0.0.1 of embplant_pt and embplant_mt, you can choose any one of the following code blocks to install:

  1. Use curl to download the released compressed file (ca. 20 MB -> 80 MB):
curl -L https://github.com/Kinggerm/GetOrganelleDB/releases/download/0.0.1/v0.0.1.tar.gz | tar zx
get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./0.0.1
  1. Use svn to download part of the repository (ca. 80 MB):
svn co https://github.com/Kinggerm/GetOrganelleDB/trunk/0.0.0
get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./0.0.1
  1. Use git clone to clone the entire repository (ca. 100 MB):
git clone https://github.com/Kinggerm/GetOrganelleDB
get_organelle_config.py -a embplant_pt,embplant_mt --use-local ./GetOrganelleDB/0.0.1