Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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 wrote: >

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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 wrote: > Hi Tin, > > I deleted the fork since as you

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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 wrote: > Hi again, > > I'm pretty sure I

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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 +, Duy Tin Truong wrote: > Hi Andreas, > > Thanks for your

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

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 wrote: > Hi

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Tin, On Fri, Aug 12, 2016 at 03:30:25PM +, 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

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, > 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

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Tin, On Fri, Aug 12, 2016 at 01:56:39PM +, Duy Tin Truong wrote: > Yes, that is fine for me. Just a small comment, metaphlan2-data will depend > on bowtie2 so that you can have bowtie2 to convert the fasta file. Yes, that's obvious. > In addition, this is the list of dependencies for

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, Yes, that is fine for me. Just a small comment, metaphlan2-data will depend on bowtie2 so that you can have bowtie2 to convert the fasta file. In addition, this is the list of dependencies for metaphlan2 in case you need:

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Duy, On Thu, Aug 11, 2016 at 05:03:20AM +, Duy Tin Truong wrote: > We have discussed the plan but unfortunately, we do not have enough > resource for that task now. In addition, redesigning the source structure > requires us to change all tutorials and that is quite expensive for us and >

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, We have discussed the plan but unfortunately, we do not have enough resource for that task now. In addition, redesigning the source structure requires us to change all tutorials and that is quite expensive for us and users now. We will inform you when we can separate them. Currently,

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi again, On Sat, Aug 06, 2016 at 01:47:23PM +, Duy Tin Truong wrote: > Regarding the separation code and data issue, I will discuss with Nicola > next Monday and let you know. any plan how to provide code and data in the future? Kind regards Andreas. -- http://fam-tille.de

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, I meant the latest version of the repository fit with the tutorial on the repository. If you used the older version (old names), I am afraid users will have some problems when following the tutorial. Regarding the separation code and data issue, I will discuss with Nicola next Monday

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Tin, I need to admit that I can not parse the information you gave in your mail. It is also not really connected to my next mail (which is archived here https://lists.debian.org/debian-med/2016/08/msg00040.html ) about the separation of code and data. Kind regards Andreas. On Thu,

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, If you can use the latest version with the name changes as I mentioned, it would fit better with the updated tutorial on the metaphlan2 repository. Thanks, Tin On Thu, Aug 4, 2016 at 1:28 PM Nicola Segata wrote: > Hi Andreas, > yes, it is likely that the

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, yes, it is likely that the code will be frequently updated, but the big database file will change only rarely (for sure no more frequently than once a year). thanks Nicola On Thu, Aug 4, 2016 at 12:46 PM Andreas Tille wrote: > Hi again, > > On Thu, Aug 04, 2016 at

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi again, On Thu, Aug 04, 2016 at 08:10:29AM +, Nicola Segata wrote: > Makes sense to me! https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833388#15 If you read the discussion it seems that my suggestion to ship the fasta file inside the Debian package and let the postinst do the

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Makes sense to me! thanks Nicola On Thu, Aug 4, 2016 at 8:18 AM Andreas Tille wrote: > Hi Nicola, > > On Wed, Aug 03, 2016 at 08:51:33PM +, Nicola Segata wrote: > > Great, thanks Andreas. We provide the "*.bt2" files so that the user can > > run BowTie2 internally to

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Nicola, On Wed, Aug 03, 2016 at 08:51:33PM +, Nicola Segata wrote: > Great, thanks Andreas. We provide the "*.bt2" files so that the user can > run BowTie2 internally to MetaPhlAn directly without first building the > indexes (it will take quite a bit of time). Fully agreed here. > Also,

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Great, thanks Andreas. We provide the "*.bt2" files so that the user can run BowTie2 internally to MetaPhlAn directly without first building the indexes (it will take quite a bit of time). Also, the indexes are smaller in size than the sequence file... cheers Nicola On Wed, Aug 3, 2016 at 6:08

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Tin, On Wed, Aug 03, 2016 at 02:01:01PM +, Duy Tin Truong wrote: > > - Tin can also provide more info about the binary data in db_v20. The files > > ending with "bt2" are created using a script in the Bowtie2 package > > (bowtie2-build) using a sequence file Tin can provide (it can also be

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, Thanks for you work. I answer your questions as bellow: - some small fixes: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch?view=markup -> fixed - some spelling issues https://anonscm.debian.

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Nicola, thanks for your answer. On Tue, Aug 02, 2016 at 04:32:31PM +, Nicola Segata wrote: > Hi Andreas, > sorry for the delay in replying. I did get your last two emails but it > seems the fist one (On Mon, Jul 25, 2016 at 09:45:57PM) never arrived. Hmmm, sad that there seems to be

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Andreas, sorry for the delay in replying. I did get your last two emails but it seems the fist one (On Mon, Jul 25, 2016 at 09:45:57PM) never arrived. Thanks so much for the suggestions. Tin, can you take a look at these two sets of suggestions and update the source code of MetaPhlAn2

Re: Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi Nicola, did you received the two mails about licensing (+ in the case of lefse a description) ? Kind regards Andreas. On Wed, Jul 27, 2016 at 09:09:01AM +0200, Andreas Tille wrote: > Hi again, > > I have another question in addition to the one below. I was packaging > MetaPhLan2 to

Description for lefse tools (Was: Origin of data files in MetaPhLan2)

Hi again, I have another question in addition to the one below. I was packaging MetaPhLan2 to make use of it in my final target package for metaBIT[1] which in addition is using some Python code I've found here https://bitbucket.org/nsegata/lefse This code has neither any description I