Hi Tin, Perfect! The accepted pull requests are what I was referring to in my prior email. Sorry I was unclear! The changes were all merged in main before I removed my forked repository.
Thank you, Lauren On Wed, Aug 31, 2016 at 1:33 PM, Duy Tin Truong <[email protected]> wrote: > Thanks Lauren. Actually, I only merged the requests that you sent and the > files you uploaded in the Download page are still in the main repository. > > Cheers, > Tin > > On Wed, Aug 31, 2016 at 6:43 PM Lauren McIver <[email protected]> > wrote: > >> Hi Tin, >> >> I deleted the fork since as you mentioned the changes were merged into >> the main repository. >> >> Thanks! >> Lauren >> >> >> On Wed, Aug 31, 2016 at 1:31 AM, Duy Tin Truong <[email protected]> >> wrote: >> >>> Hi Andreas, >>> >>> That is the fork from Lauren and we merged the change into the main >>> repository. The main repository is still at: >>> https://bitbucket.org/biobakery/metaphlan2/overview >>> >>> Thanks, >>> Tin >>> >>> On Wed, Aug 31, 2016 at 9:11 AM Andreas Tille <[email protected]> wrote: >>> >>>> Hi again, >>>> >>>> I'm pretty sure I have seen the 2.6.0 tag right after your mail. I was >>>> a bit busy since then and wanted to have a look now. I noticed that >>>> metaphlan2 moved to another user on bitbucket and >>>> >>>> https://bitbucket.org/ljmciver/metaphlan2/downloads?tab=tags >>>> >>>> only shows 2.5.0 as latest tag. >>>> >>>> Am I missing something? >>>> >>>> Kind regards >>>> >>>> Andreas. >>>> >>>> On Fri, Aug 19, 2016 at 12:18:31PM +0200, Andreas Tille wrote: >>>> > Hi Duy, >>>> > >>>> > thanks for the information. It might take some time since I'll be a >>>> bit >>>> > offline-ish next week but now I know what the correct target for the >>>> > package will be. >>>> > >>>> > Kind regards >>>> > >>>> > Andreas. >>>> > >>>> > On Fri, Aug 19, 2016 at 07:17:25AM +0000, Duy Tin Truong wrote: >>>> > > Hi Andreas, >>>> > > >>>> > > Thanks for your explanation. We have officially updated metaphlan2 >>>> to >>>> > > version 2.6.0 as shown in tags. >>>> > > So, when it is convenient for you, please help to add the package >>>> of this >>>> > > new version. >>>> > > >>>> > > Many thanks, >>>> > > Tin >>>> > > >>>> > > On Fri, Aug 12, 2016 at 6:31 PM Andreas Tille <[email protected]> >>>> wrote: >>>> > > >>>> > > > Hi Tin, >>>> > > > >>>> > > > On Fri, Aug 12, 2016 at 03:30:25PM +0000, Duy Tin Truong wrote: >>>> > > > > > However the hint ot hclust2[1] is helpful. Unfortunately I >>>> can not >>>> > > > find >>>> > > > > > any description for this software. Since you might have some >>>> > > > influence on >>>> > > > > > this it would be great to provide a hint where I can find a >>>> > > > description for >>>> > > > > > a potential package. >>>> > > > > > >>>> > > > > hclust2 is used to plot heat-maps and not directly used in >>>> metaphlan2.py >>>> > > > or >>>> > > > > strainphlan.py. In other words, metaphlan2 does not depend >>>> tightly on >>>> > > > this >>>> > > > > tool. However, I will update the wiki page later. >>>> > > > >>>> > > > Sounds like a neat tool anyway - so if there is a description I >>>> could >>>> > > > provide a package. >>>> > > > >>>> > > > > > > and here for strainphlan (another brother tool uses the >>>> same database >>>> > > > > > with >>>> > > > > > > metaphlan2 and both are in the same repository and should go >>>> > > > together, >>>> > > > > > > strainphlan is in strainphlan.py and metaphlan2 is in >>>> metaphlan2.py): >>>> > > > > > > >>>> > > > > > >>>> > > > https://bitbucket.org/biobakery/metaphlan2#markdown- >>>> header-pre-requisites_1 >>>> > > > > > >>>> > > > > > Well, the download file for metaphlan2 version 2.5 has >>>> strainer_src and >>>> > > > > > metaphlan2_strainer.py - is this what you mean? >>>> > > > > > >>>> > > > > Yes, strainer_src is now strainphlan_src and >>>> metaphlan2_strainer.py is >>>> > > > now >>>> > > > > strainphlan.py. As I mentioned before, it is better to use the >>>> latest >>>> > > > > version of the repository now because the tutorial now fits >>>> with the new >>>> > > > > names: >>>> > > > > >>>> > > > https://bitbucket.org/biobakery/metaphlan2#markdown- >>>> header-metagenomic-strain-level-population-genomics >>>> > > > > >>>> > > > > and we may not change them again :). >>>> > > > >>>> > > > So *if* you want to let users use the latest state of the >>>> repository why >>>> > > > don't you do a new versioned release to make it official. Debian >>>> uses a >>>> > > > system to check web pages for versioned releases. We can not >>>> sneak into >>>> > > > each repository nor wild guessing if it is a stable commit or >>>> not. Is >>>> > > > there any reason not to release say version 2.6 or 2.5.1 or >>>> whatever? >>>> > > > >>>> > > > Kind regards >>>> > > > >>>> > > > Andreas. >>>> > > > >>>> > > > > > [1] https://bitbucket.org/nsegata/hclust2 >>>> > > > >>>> > > > -- >>>> > > > http://fam-tille.de >>>> > > > >>>> > >>>> > -- >>>> > http://fam-tille.de >>>> > >>>> > >>>> >>>> -- >>>> http://fam-tille.de >>>> >>> >>
