Hi Nicola, On Wed, May 25, 2016 at 07:56:08AM +0000, Nicola Segata wrote: > Hi Adreas, > we recently updated PhyloPhlAn to support other usearch versions. I'm > CC'ing Francesco (the lead on the project) which can be more accurate on > which usearch version we need for the last version of PhyloPhlAn.
It would be nice to get some confirmation about the usearch version. > Regarding other software I think it would be fantastic to have MetaPhlAn2 > as a Debian package. It's here: https://bitbucket.org/biobakery/metaphlan2 . > It is widely used and stable (although we are further and actively > developing it) and published a couple of times in Nat Methods. I had a look into this. It contains quite large binary data chunks. Before I can seriously attempt to package this I would need to know where and how theses data are obtained from, how to possibly change the data (if this makes sense at all - if not why not) and what the copyright of the data would be. Otherwise Debian ftpmaster will refuse the package to be uploaded. > Another software we developed that would be great to have as a Debian > package is GraPhlAn (https://bitbucket.org/nsegata/graphlan/wiki/Home) > (Described here https://peerj.com/articles/1029/). It's a package to > produce nice graphical representation of phylogenetic trees. That's a really nice one. :-) I injected packaging code into our packaging version control system. However, when doing so I noticed that I need to package pyphlan[1] first. I committed the needed packaging code into our packaging Git and can confirm that the packaging of graphlan works together with this precondition. Before I can upload pyphlan to the Debian mirror it would be great to have at least a minimum three lines description, what the package is actually doing. I found something in the code that there are functions you would like to see in Biopython (did you contacted Biopython authors about this - I learned they are very responsive and open for enhancements) but I have no real clue what the code is doing - except that its a precondition for graphlan. So please provide some sensible description. Another nice thing would to add a version tag to bitbucket. This would enable me to find a proper Debian package version which is currently simply the date of the youngest file inside the download archive. > Importantly, these two packages don't use any proprietary software so it > should be easier to package them than PhyloPhlAn. You are right but as I said above the binary data need some explanation. > Let us know if you have any question and if we can help you somehow! Thanks a lot for your nice hints. We like to have this kind of cooperation with upstream software authors. Kind regards Andreas. [1] https://bitbucket.org/nsegata/pyphlan [2] https://anonscm.debian.org/cgit/debian-med/python-pyphlan.git -- http://fam-tille.de