BioSmalltalk is an Open-Source (MIT-licensed) library for Bioinformatics using Smalltalk (currently Pharo).
There are several ways to install BioSmalltalk. At minimum, you need a working Pharo virtual image installed in a system. Check the Pharo website for installation information regarding the Pharo Open-Source system. To paste the following expressions inside Pharo, open a "Playground" window with (Cmd + O + I) or by clicking an empty area in the Pharo window and select Tools -> Playground.
To evaluate a expression, click on the upper right green arrow or highlight the script code and right click for options.
For additional help using Pharo please check the excellent free Pharo books, the awesome-pharo lists and the wiki. For a quick reference of the syntax, check the Pharo Cheat Sheet
You can uncomment the specific loading group in the following expression by removing the # prepended character, and add it to the group currently uncommented. Check the installation matrix above to know about the options. The script should be evaluated inside the Pharo image. The current Pharo version 8.x is supported.
EpMonitor disableDuring: [
Metacello new
onConflictUseLoaded;
onWarningLog;
repository: 'github://hernanmd/biosmalltalk/repository';
baseline: 'BioSmalltalk';
load ].In case of problems check Troubleshoot Install
If you want to add BioSmalltalk to your Metacello Baselines or Configurations, copy and paste the following expression:
" ... "
spec
baseline: 'BioSmalltalk'
with: [ spec repository: 'github://hernanmd/BioSmalltalk/repository' ];
" ... "
If you want to add a BioSmalltalk installation group to your Metacello Baselines or Configurations, copy and paste the following expression, replacing Basic with the group of your interest:
" ... "
spec
baseline: 'BioSmalltalk'
with: [ spec load: #('Basic'); repository: 'github://hernanmd/BioSmalltalk/repository' ];
" ... "
Please see BioSmalltalk web site for documentation
Working on your first Pull Request? You can learn how from this free series How to Contribute to an Open Source Project on GitHub
If you have discovered a bug or have a feature suggestion, feel free to create an issue on Github. If you'd like to make some changes yourself, see the following:
- Fork this repository to your own GitHub account and then clone it to your local device
- Do some modifications
- Test.
- Add to add yourself as author below.
- Finally, submit a pull request with your changes!
- This project follows the all-contributors specification. Contributions of any kind are welcome!
This software is licensed under the MIT License.
Copyright Hernán Morales, 2011-2022.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.