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Initialization
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.
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.
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:
- Use
curlto 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
- 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
- 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