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 stage as it is now largely superseded by HISAT2 which provides the 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 efficient way. and a statement from one of its co-authors [2] > Please stop using Tophat. Cole and I developed the > method in *2008*. It was greatly improved in TopHat2 then HISAT > & HISAT2. There is no reason to use it anymore. I have been > saying this for years yet it has more citations this year than last I think we'd be doing users a favor by removing it from the archive. If in the future anyone wants to replicate old results based on tophat, they could build a container off of snapshot.debian.org. Are there any objections? regards Afif 1. https://ccb.jhu.edu/software/tophat/index.shtml 2. https://twitter.com/lpachter/status/937055346987712512 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
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 lot for fixing this. 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 -DCHECK_FUNCTION_EXISTS=pthread_ create -Wl,-z,relro -Wl,-z,now CMakeFiles/cmTC_de0fb.dir/CheckFunctionExists.c.o -o cmTC_de0fb -rdynamic -lpthreads /usr/bin/ld: cannot find -lpthreads collect2: error: ld returned 1 exit status I assume that would be easy to fix but got not help so far. I found some hint in the web to add find_package(Threads) but I either did it on the wrong place or it does not help. I'd love if we could at least upload this version which is currently also superseeded by version 0.9.1. It would be even better but after I gave it a try and tried to fight through the hell of patches I gave up since I did not even managed to get the cmake configure step successful. Do you have any idea how to fix the pthreads issue and then we could apply your patch to 0.8.0 (if needed)? Kind regards Andreas. -- http://fam-tille.de
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 something like this. Kind regards Andreas. -- http://fam-tille.de
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 -DCHECK_FUNCTION_EXISTS=pthread_ > create -Wl,-z,relro -Wl,- > z,now CMakeFiles/cmTC_de0fb.dir/CheckFunctionExists.c.o -o > cmTC_de0fb -rdynamic -lpthreads > /usr/bin/ld: cannot find -lpthreads > collect2: error: ld returned 1 exit status > > > I assume that would be easy to fix but got not help so far. I found > some hint in the web to add > > find_package(Threads) > > but I either did it on the wrong place or it does not help. The problem is, I didn't even get that far, as I pointes out, a file was missing to compile the whole thing. I'll try to give it another shot by first compiling the origial version to see if I get it to work at all, end then re-applying the patches. Best, Gert
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 making sure that google indexes the announcement as the first result when someone searches for it. Source: sysadmin in bioinformatics, also masters students in bioinformatics, I was just instructed last Tuesday on how to use tophat in Ubuntu. Best Regards, George Marselis From: Andreas Tille Sent: Saturday, December 16, 2017 11:31 AM To: debian-med@lists.debian.org Subject: 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 something like this. Kind regards Andreas. -- http://fam-tille.de
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 > comfortable with it, some sort of way of making sure that google indexes > the announcement as the first result when someone searches for it. I agree, that some people might be dependent on tophat and we should not remove an essential components of their workflow. If we want to remove tophat, we should make it print a warning like “[WARNING] Stop using tophat: http://some-explanatory.url/”. After that has been out for a few months, we could make tophat always exit with a non-zero state as to intentionally break ppls. workflows and make them read the error message. Finally, after such a grace period, removal might be valid. Best, Fabian
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, 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 > > comfortable with it, some sort of way of making sure that google indexes > > the announcement as the first result when someone searches for it. > > > I agree, that some people might be dependent on tophat and we should not > remove an essential components of their workflow. If we want to remove > tophat, we should make it print a warning like “[WARNING] Stop using > tophat: http://some-explanatory.url/”. After that has been out for a few > months, we could make tophat always exit with a non-zero state as to > intentionally break ppls. workflows and make them read the error > message. Finally, after such a grace period, removal might be valid. > > Best, > Fabian >
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 like this if you will not manage. > > Kind regards > >Andreas. > the updated version of bowtie is in repository. Best regards, Alex
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 should provide kind of a sensible >"migration path" and add "Replaces: tophat" to hisat2 or something like >this. > Ack. Although I don't believe Replaces: is correct here (looking at Debian policy). Maybe a transitional package is needed, which would have to sit through another stable release cycle. That would also satisfy the concerns about notification time that the others brought up on this thread. regards Afif
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. > > Ack. Although I don't believe Replaces: is correct here (looking at Debian > policy). Its definitely incorrect. However, we need to make sure that users who had installed tophat get hisat2 installed. > Maybe a transitional package is needed, which would have to sit through > another stable release cycle. That would also satisfy the concerns about > notification time that the others brought up on this thread. After reading this thread I think the better way to go is: 1. tophat Depends hisat2 (solves the issue that the replacement will be installed 2. provide instead of /usr/bin/tophat a shell script issuing a warning first before the actual tophat call What about this? Kind regards Andreas. -- http://fam-tille.de
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 of a sensible >> >"migration path" and add "Replaces: tophat" to hisat2 or something >like >> >this. >> >> Ack. Although I don't believe Replaces: is correct here (looking at >Debian policy). > >Its definitely incorrect. However, we need to make sure that users who >had installed tophat get hisat2 installed. > >> Maybe a transitional package is needed, which would have to sit >through another stable release cycle. That would also satisfy the >concerns about notification time that the others brought up on this >thread. > >After reading this thread I think the better way to go is: > > 1. tophat Depends hisat2 (solves the issue that the replacement > will be installed > 2. provide instead of /usr/bin/tophat a shell script issuing > a warning first before the actual tophat call > >What about this? > That looks like a transitional package. I'm for it. regards Afif
