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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Licensing #9

Open marcelauliano opened 4 years ago

marcelauliano commented 4 years ago

Hey Remio, Congrats, this is a great pipeline!

I would like to implement some steps of your MitoFinder in a pipeline of mine. If your intention is to have it free, could you add a MIT or similar license to your pipeline?

Thank you! Marcela.

RemiAllio commented 4 years ago

Hi Marcela,

The license is included in each script file.

For example, in the file "mitofinder", you can find the following license:

''' Copyright (c) 2019 Remi Allio - ISEM/CNRS & Alex Schomaker-Bastos - LAMPADA/UFRJ 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. '''

Is that sufficient ? Do you want me to add a license file in the repository ? Let me know because I don't have any experience with that.

Cheers, Rémi

marcelauliano commented 4 years ago

Hey Remio, Thanks for your answer!

I have add mitofinder here https://github.com/marcelauliano/MitoHiFi

If you are ok with the licenses on each script, its ok with me. Otherwise, maybe repeating the free license on your README would be useful too? =) Hope you and Fred are well!

ps: I worked many years with Alex. He was a very good friend and a amazing student. I miss him very much

RemiAllio commented 4 years ago

Hey Marcela,

Thank you for the update! I have just two little points: 1- Please, could you replace "mitoFinder" by "MitoFinder" 2- It might be useful to include citation information for the programs to your pipeline as I did in my README? Of course, in your case, you don't need to add the citations for the different assemblers (MEGAHIT, metaSPAdes and IDBA-UD) but it would be nice to include citations at least for MitoFinder and Arwen.

Thanks in advance, Cheers, Rémi

ps: I haven't had the chance to meet Alex but I've heard a lot of good things about him. I'm sorry for your loss.