removing tophat from Debian

Hi, all, Given the statement from the website [1] > Please note that TopHat has entered a low maintenance, low support > stage as it is now largely superseded by HISAT2 which provides the > same core functionality (i.e. spliced alignment of RNA-Seq reads), > in a more accurate and much more

Re: removing tophat from Debian

Hi Afif, On Sat, Dec 16, 2017 at 03:18:05AM -0500, Afif Elghraoui wrote: > > Are there any objections? Since I'm not a user of all this software I do not have any objections. However, I wonder whether we should provide kind of a sensible "migration path" and add "Replaces: tophat" to hisat2 or

Re: Salmon

Hi Gert, On Wed, Dec 13, 2017 at 11:44:18AM +0100, Gert Wollny wrote: > since in the build-tree there is also a version 0.8, and I had to give > up fixing that version - there was some include "FrugalBooMap.hpp" > missing, I've fixed the RC bug in an new branch: "version-7.2". At first thanks a

RE: removing tophat from Debian

Second that motion. There are *plenty* of bioinformaticians and sysadmins, especially downstream of Debian who will say “I need tophat”, without being able to explain why they do. Migration path, big announcement, large time path so everybody gets comfortable with it, some sort of way of

Re: Salmon

Am Samstag, den 16.12.2017, 10:28 +0100 schrieb Andreas Tille: > Hi Gert, > > I once injected version 0.8.0 where I ended up with  > >   /usr/bin/cc  -g -O2 -fdebug-prefix-map=/build/salmon-0.8.0+ds1=. > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2

Re: removing tophat from Debian

Hi, On 16.12.2017 15:40, geo...@marsel.is wrote: > There are **plenty** of bioinformaticians and sysadmins, especially > downstream of Debian who will say “I need tophat”, without being able to > explain why they do. > >   > > Migration path, big announcement, large time path so everybody gets

Re: removing tophat from Debian

that also means there is a need for the maintainers of packages such as galaxy or taverna to be notified and/or make sure when used in a pipeline tophat throws a yuge error. On Sat, Dec 16, 2017 at 8:00 PM, Fabian Klötzl wrote: > Hi, > > On 16.12.2017 15:40,

Re: removing tophat from Debian

On December 16, 2017 1:31:01 AM PST, Andreas Tille wrote: >Hi Afif, > >On Sat, Dec 16, 2017 at 03:18:05AM -0500, Afif Elghraoui wrote: >> >> Are there any objections? > >Since I'm not a user of all this software I do not have any objections. >However, I wonder whether we

Re: removing tophat from Debian

Hi, Andreas, On December 16, 2017 1:15:16 PM PST, Andreas Tille wrote: >Hi Afif, > >On Sat, Dec 16, 2017 at 12:31:28PM -0800, Afif Elghraoui wrote: >> >Since I'm not a user of all this software I do not have any >objections. >> >However, I wonder whether we should provide kind

Re: RFS: bowtie/1.2.1.1+dfsg-1

Hi All, >> A new version has been released. >> https://github.com/BenLangmead/bowtie/releases >> >> Please also note the license change. > > Thanks a lot for both hints. You can feel free to update the packaging > in Git yourself if you want to. Or Alex? Please throw ENOTIME or > something

Re: removing tophat from Debian

Hi Afif, On Sat, Dec 16, 2017 at 12:31:28PM -0800, Afif Elghraoui wrote: > >Since I'm not a user of all this software I do not have any objections. > >However, I wonder whether we should provide kind of a sensible > >"migration path" and add "Replaces: tophat" to hisat2 or something like > >this.