A commandline and GUI tool for the creation of Artemis/Artemis Comparison Tool files.
Project description
Oread
/ˈɔːrɪad/
A commandline and GUI tool for the creation of Artemis/Artemis Comparison Tool files.
Installation
Presently, this package doesn't require installation, it does have several dependencies though:
- Install a
miniconda
distribution (or anything that allows access to apythonw
binary butminiconda
is recommended (later this tool may be installable viaconda
) - Install
biopython
(very easy viaconda
with$ conda install -c bioconda biopython
) - Ensure you have the BLAST+ suite installed (NOT legacy BLAST). Also very easy via
conda
:$ conda install -c bioconda blast
- Finally, the GUI depends on the non-standard module
Gooey
. Install it viaconda
with:$conda install -c krrishnarraj gooey
or viapip
withpythonw -m pip install gooey
Running
So far this has only been tested on MacOS. For this, a "framework" version of python is needed.
This can be installed via conda
which is strongly recommended, and then the script run with the
pythonw
binary:
$ pythonw Artemisia.py
This will open the window. If you set the Artemisia.py
script to be executable (it should already be)
and to open with Terminal
by default (select the file, Command+I
, then alter the defaults), you can launch
with a double click.
The program can also be run from the commandline by providing the --ignore-gooey
option to disable the GUI.
$ python Oread.py --ignore-gooey <...options...>
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