add omssa, MSFragger, MaraCluster - Githubissues

bioconda / bioconda-recipes

Conda recipes for the bioconda channel.

https://bioconda.github.io

MIT License

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add omssa, MSFragger, MaraCluster #18953

Open bernt-matthias opened 5 years ago

bernt-matthias commented 5 years ago

[x] OMSSA: Even if its old some some software like OpenMS still uses it. ftp://ftp.ncbi.nlm.nih.gov/pub/lewisg/omssa/2.1.9/
- [x] recipe https://github.com/bioconda/bioconda-recipes/pull/19181
[x] LuciPhor2: http://luciphor2.sourceforge.net/
- [x] provide stable link via depot https://github.com/galaxyproject/cargo-port/pull/164
- [x] recipe https://github.com/bioconda/bioconda-recipes/pull/19551
[ ] MaraCluster https://github.com/statisticalbiotechnology/maracluster
- [ ] https://github.com/bioconda/bioconda-recipes/pull/21472
- [ ] https://github.com/bioconda/bioconda-recipes/pull/19219
[x] percolator https://github.com/bioconda/bioconda-recipes/pull/16532
[x] Inspect. Maybe Available from the authors https://cseweb.ucsd.edu/classes/sp10/cse283/notes/inspect.pdf
- personal communication with author V. Bafna: "InsPect is no longer maintained as there are many better tools including MS-GF+"
[x] SpectraST
- exists as conda package (tpp)
- source is included in the huge TPP pipeline distribution http://tools.proteomecenter.org/wiki/index.php?title=SpectraST

Probably not possible due to non suitable licence (I still list them here for my reference)

[ ] Mascot Commercial http://www.matrixscience.com/
[ ] MSFragger https://github.com/Nesvilab/MSFragger
- probably not possible https://github.com/Nesvilab/MSFragger/issues/51
- https://github.com/bioconda/bioconda-recipes/pull/45127
[ ] Novor http://www.rapidnovor.org/novor

glormph commented 4 years ago

I was planning to have a go at maracluster as well. But my C++-fu and my time for it are both a bit short. At least seeing this can be a good spur, maybe it'll work out this time.