Fragmet library can be used.

lenarother / moderna

A program for comparative RNA modeling.

GNU General Public License v3.0

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Fragmet library can be used. #56

Closed lenarother closed 10 years ago

lenarother commented 10 years ago

Now ModernaFragment.lib and folder with pdb files are locally in the repository. Reason: files are big. ModeRNA gets big. Effects:

when somebody clone the repo ---> tests won't pass
when somebody downloads release ---> cannot insert fragments automatically, automatic modelling of alignment with gaps will result in incomplete model.

Proposed solutions:

make separate pip package FragmentLibrary.
include library in ModeRNA repo (this one).
store the files online.

Do you have any other solutions or favourite one from the above?

lenarother commented 10 years ago

Paweł, do you have opinion on that?

lenarother commented 10 years ago

I think this one needs to be solved to get Travis pass.

lenarother commented 10 years ago

Opinion of other programmers not involved in the project: add directly in the repo, don't hassle on details, it's not the size to worry about.

cosi1 commented 10 years ago

The first thing that came to my mind was to make it an "add-on", automatically downloaded when installing ModeRNA, but then I thought: ".pdb files are easily compressible. Why not try to compress them with some really good tool (like 7z maybe)?" They even don't need to be uncompressed after the installation - ModeRNA could unpack them on-the-fly when needed.

Does it make sense to you?

krother commented 10 years ago

Thanks for your quick response.

A .tar.gz brings the size of the library down to 25% already. How much more would 7z bring us - and would it speed up development? I am a little concerned of two things: 1) adding a dependency - I don't know whether Python can read 7z on all operating systems. 2) Zipped PDB files can't be edited manually (we did this a lot initially, but currently nobody does).

Git itself zips stuff internally by default, so we could add the files so that tests pass (speeds up development), and add your zip suggestion as a new issue (might speed up download or program or both).

lenarother commented 10 years ago

Thanks PP and KR !

cosi1 commented 10 years ago

Well, one more idea then: if the fragment library as a whole isn't always needed and only single files are used when inserting certain fragments, maybe it would make sense to download them successively when needed (and after that not remove them)? This would help avoid the "huge-download-at-once" problem, and for those who don't want (or can't) download single files, there could be a whole package.

What do you think?

lenarother commented 10 years ago

Thanks! I like this one! Then we could use directly PDB.

cosi1 commented 10 years ago

I'm glad you like it :-)

The fragment library could be a distinct project, either kept on GitHub or on a dedicated server (and mirrored!). Then it would be easier to keep it up-to-date and maybe even reuse in some other projects...

lenarother commented 10 years ago

For now both (lib file and pdb folder) added to the repo.