Re: removing tophat from Debian

[Afif Elghraoui]

On December 20, 2017 5:17:20 AM EST, Michael Crusoe  
wrote:
>2017-12-16 10:18 GMT+02:00 Afif Elghraoui :
>
>> 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 stage as it is now largely superseded by HISAT2 which provides the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
>>
>
>This statement is about TopHat 2, which is what is in the Debian
>package
>tophat
>
>
>> 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
>>
>
>This more strongly worded statement is about TopHat 1, which is not in
>Debian.
>

The summary of the statement is that hisat2 is the only one of those 4 that 
isn't obsolete, and therefore that it's the only one of those 4 that should be 
used.

>We should retain TopHat2, perhaps with a note about HISAT2.
>

I think tophat2 (and hisat1 if we have it) should also be removed. We should 
get upstream involved if you still disagree.

regards
Afif

Exclicitly or "implicitly" mark architectures a packages does not build

[Andreas Tille]

Hi,

in spring several packages from Debian Med team received "FTBFS on i386:
unsatisfiable build-dependencies" bug reports (sorry for not caring
earlier).  An "example bug" #860655 is in CC.  Originally these bugs
were filed with severity serious but at it was pointed out by Gianfranco
Costamagna[1] the severity of this issue for packages that were never
built on a certain architecture are not serious.  So the severity of all
these bugs was decreased to wishlist.

Since we also intend to care for wishlist bugs I'm now wondering the
following:  Yes, there are packages that do not build on a certain
architecture due to missing Build-Depends.  I could exclude these
architectures from the list of architectures in d/control.  However, as
far as I understood that's rather a bad idea since once the
Build-Depends might become available the package could easily build.

In some cases we even added a Build-Depends which actually is not really
a Build-Depends but just a Depends of the package but there is no point
to build the package if it can not be installed afterwards (see for
instance gasic[2]).

So as far as I see #860655 there is no sensible means to fix it properly
and I'm tempted to close it (since I also do not see any sense in
tagging it wontfix).  May be it needs to be said that we do not have the
manpower to fix each and every piece of code to make sure all
Build-Depends build on every architecture neither does it make sense
technically to for instance have gene sequencing software on outdated
hardware available.  Some code just needs 64 bit and upstream will not
support other hardware.

Am I missing something?

Kind regards

   Andreas.

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=860652#15
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=873859#15

-- 
http://fam-tille.de

Re: removing tophat from Debian

[Michael Crusoe]

2017-12-16 10:18 GMT+02:00 Afif Elghraoui :

> 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
>

This statement is about TopHat 2, which is what is in the Debian package
tophat


> 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
>

This more strongly worded statement is about TopHat 1, which is not in
Debian.

We should retain TopHat2, perhaps with a note about HISAT2.


>
> 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
>
>


-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108