[PATCH] gnu: Add r-qtl.

[PATCH] gnu: Add r-qtl.

[Pjotr Prins]

* gnu/packages/bioinformatics.scm (r-qtl): New variable.
---
 gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a13fd7a..cc6a418 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -28,6 +28,7 @@
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
   #:use-module (guix build-system ruby)
+  #:use-module (guix build-system r)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
@@ -2700,3 +2701,24 @@ position for indels.  Bio-locus allows users to store this chr+pos or
 chr+pos+alt information in a database.")
     (home-page "https://github.com/pjotrp/bio-locus")
     (license license:expat)))
+
+(define-public r-qtl
+  (package
+    (name "r-qtl")
+    (version "1.37-11")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append
+              "mirror://cran/src/contrib/qtl_"
+              version ".tar.gz"))
+        (sha256
+          (base32
+           "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi"))))
+    (build-system r-build-system)
+    (home-page "http://www.rqtl.org")
+    (synopsis "Tools for Analyzing QTL Experiments")
+    (description "Bio-statistics library for analysis of experimental
+crosses to identify genes (called quantitative trait loci, QTLs)
+contributing to variation in quantitative traits.")
+    (license license:gpl3+)))
-- 
2.4.3

Re: [PATCH] gnu: Add r-qtl.

[Mathieu Lirzin]

Pjotr Prins <pjotr.public12@thebird.nl> writes:

> * gnu/packages/bioinformatics.scm (r-qtl): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
>  1 file changed, 22 insertions(+)

[...]

> +    (build-system r-build-system)
> +    (home-page "http://www.rqtl.org")
> +    (synopsis "Tools for Analyzing QTL Experiments")
                                      ^^^
Could you modify this be more explicit for a non-specialized audience?
(Also capitalize only the first word.)

> +    (description "Bio-statistics library for analysis of experimental
> +crosses to identify genes (called quantitative trait loci, QTLs)
> +contributing to variation in quantitative traits.")
> +    (license license:gpl3+)))

I don't understand the meaning but on the form side I think QTL sould be
introduced in a full sentence like this "... Quantitative Trait Loci
(QTL) ...".  Can you try to make it more verbose?

Otherwise LGTM.  Thanks.

--
Mathieu Lirzin

Re: [PATCH] gnu: Add r-qtl.

[Pjotr Prins]

Package descriptions I follow are the same as those by the software
developers. If people care about jargon feel free to fix it.

I am happy with the original descriptions from the software authors.
Spelling it out won't help any users.

Personally I don't see why we have to stop this patch.

Pj.

On Thu, Sep 17, 2015 at 07:18:10PM +0200, Mathieu Lirzin wrote:
> Pjotr Prins <pjotr.public12@thebird.nl> writes:
> 
> > * gnu/packages/bioinformatics.scm (r-qtl): New variable.
> > ---
> >  gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++
> >  1 file changed, 22 insertions(+)
> 
> [...]
> 
> > +    (build-system r-build-system)
> > +    (home-page "http://www.rqtl.org")
> > +    (synopsis "Tools for Analyzing QTL Experiments")
>                                       ^^^
> Could you modify this be more explicit for a non-specialized audience?
> (Also capitalize only the first word.)
> 
> > +    (description "Bio-statistics library for analysis of experimental
> > +crosses to identify genes (called quantitative trait loci, QTLs)
> > +contributing to variation in quantitative traits.")
> > +    (license license:gpl3+)))
> 
> I don't understand the meaning but on the form side I think QTL sould be
> introduced in a full sentence like this "... Quantitative Trait Loci
> (QTL) ...".  Can you try to make it more verbose?
> 
> Otherwise LGTM.  Thanks.
> 
> --
> Mathieu Lirzin
> 

-- 

Re: [PATCH] gnu: Add r-qtl.

[Ludovic Courtès]

Pjotr Prins <pjotr.public12@thebird.nl> skribis:

> Package descriptions I follow are the same as those by the software
> developers. If people care about jargon feel free to fix it.
>
> I am happy with the original descriptions from the software authors.
> Spelling it out won't help any users.

It will.  I tried to spell out the rationale for synopsis and
descriptions:

  https://lists.gnu.org/archive/html/guix-devel/2015-09/msg00445.html

I understand the frustration–after all you’ve already spent quite some
time on the package I suppose and the functional part is completely
fine.

However I think it’s important to work on maintaining a good level of
quality for these things.  It might look like nitpicking, but it’s
really the kind of polish that makes the tool more pleasant to use IMO.
We all benefit from it in the end.

So, what about sending an updated patch?  :-)

Thanks for your work,
Ludo’.

Re: [PATCH] gnu: Add r-qtl.

[Pjotr Prins]

I asked the author. His response is:

Titles are meant to be short, so that they can be scanned easily. If someone doesn't know what it means, it's not
 going to be of interest anyway.

The synopsis is followed immediately by the description, which seems perfectly fine to me.
though perhaps it could be changed to:

Biostatistics library for analysis of experimental crosses to identify quantitative trait loci (QTLs): genes cont
ributing to variation in quantitative traits.

...neat to see it in GNU Guix.

On Fri, Sep 18, 2015 at 11:50:24AM +0200, Ludovic Courtès wrote:
> Pjotr Prins <pjotr.public12@thebird.nl> skribis:
> 
> > Package descriptions I follow are the same as those by the software
> > developers. If people care about jargon feel free to fix it.
> >
> > I am happy with the original descriptions from the software authors.
> > Spelling it out won't help any users.
> 
> It will.  I tried to spell out the rationale for synopsis and
> descriptions:
> 
>   https://lists.gnu.org/archive/html/guix-devel/2015-09/msg00445.html
> 
> I understand the frustration–after all you’ve already spent quite some
> time on the package I suppose and the functional part is completely
> fine.
> 
> However I think it’s important to work on maintaining a good level of
> quality for these things.  It might look like nitpicking, but it’s
> really the kind of polish that makes the tool more pleasant to use IMO.
> We all benefit from it in the end.
> 
> So, what about sending an updated patch?  :-)
> 
> Thanks for your work,
> Ludo’.
> 

-- 

Re: [PATCH] gnu: Add r-qtl.

[Andreas Enge]

On Fri, Sep 18, 2015 at 01:51:15PM +0200, Pjotr Prins wrote:
> Titles are meant to be short, so that they can be scanned easily. If someone doesn't know what it means, it's not
>  going to be of interest anyway.

That is not true: Until recently I did not know what mtp is (and I still
do not really know, actually...). Until I bought an android tablet that
requires it for data transfer. Time to test Ricardo's gmtp package, by
the way :-)  If I were only interested in things I know, I would not
have much to do in my life ;-)

And sometimes I see package names that sound interesting, so it is nice
to have a synopsis and description explaining a bit what it does.

Andreas

Re: [PATCH] gnu: Add r-qtl.

[Pjotr Prins]

Well, unless someone comes up with a 'proper' description I don't 
think we'll get anywhere. Tell me what you want to see. We can't
explain the whole field of genetics in one line.

Pj.

On Fri, Sep 18, 2015 at 04:08:54PM +0200, Andreas Enge wrote:
> On Fri, Sep 18, 2015 at 01:51:15PM +0200, Pjotr Prins wrote:
> > Titles are meant to be short, so that they can be scanned easily. If someone doesn't know what it means, it's not
> >  going to be of interest anyway.
> 
> That is not true: Until recently I did not know what mtp is (and I still
> do not really know, actually...). Until I bought an android tablet that
> requires it for data transfer. Time to test Ricardo's gmtp package, by
> the way :-)  If I were only interested in things I know, I would not
> have much to do in my life ;-)
> 
> And sometimes I see package names that sound interesting, so it is nice
> to have a synopsis and description explaining a bit what it does.
> 
> Andreas
> 

-- 

Re: [PATCH] gnu: Add r-qtl.

[Andreas Enge]

On Fri, Sep 18, 2015 at 06:15:01PM +0200, Pjotr Prins wrote:
> Well, unless someone comes up with a 'proper' description I don't 
> think we'll get anywhere. Tell me what you want to see. We can't
> explain the whole field of genetics in one line.

Well, I think the package author is the most qualified to write a
description :-)  But let us break the cycle; I am ready to make a suggestion
that you as a specialist may easily improve, I suppose.

Synopsis:
R package for analyzing QTL experiments in genetics

I think it is good to have "R package" somewhere, and "genetics", which I
understand as a layman (and then I do not understand QTL, but that does not
matter since as you said, if I knew genetics, I would probably understand
QTL.) Hm, as a layman, "R package" is also not very understandable.

So how about:
Analysis tools for genetic QTL experiments in the R statistics system
Too long!

So:
Tools for genetic QTL experiments in the R system


Description: I think the point of critique was mainly that it should
consist of full sentences with a verb ("blabla is a foo" instead of "foo",
a minima). So maybe this:

"R/qtl is an extension library for the R statistics system.  It is used
to analyze experimental crosses for identifying genes contributing to
variation in quantitative traits (so-called quantitative trait loci, QTLs).

Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
identify genotyping errors, and to perform single-QTL and two-QTL,
two-dimensional genome scans."

(With some inspiration from the fine web site, of course...)

Andreas

Re: [PATCH] gnu: Add r-qtl.

[Pjotr Prins]

I checked with the author and he is fine with your version. 

Personally I think it is clear from the name that it is an R package,
so that may be superfluous. But then, who knows R ;)

Pj.


On Fri, Sep 18, 2015 at 06:56:06PM +0200, Andreas Enge wrote:
> On Fri, Sep 18, 2015 at 06:15:01PM +0200, Pjotr Prins wrote:
> > Well, unless someone comes up with a 'proper' description I don't 
> > think we'll get anywhere. Tell me what you want to see. We can't
> > explain the whole field of genetics in one line.
> 
> Well, I think the package author is the most qualified to write a
> description :-)  But let us break the cycle; I am ready to make a suggestion
> that you as a specialist may easily improve, I suppose.
> 
> Synopsis:
> R package for analyzing QTL experiments in genetics
> 
> I think it is good to have "R package" somewhere, and "genetics", which I
> understand as a layman (and then I do not understand QTL, but that does not
> matter since as you said, if I knew genetics, I would probably understand
> QTL.) Hm, as a layman, "R package" is also not very understandable.
> 
> So how about:
> Analysis tools for genetic QTL experiments in the R statistics system
> Too long!
> 
> So:
> Tools for genetic QTL experiments in the R system
> 
> 
> Description: I think the point of critique was mainly that it should
> consist of full sentences with a verb ("blabla is a foo" instead of "foo",
> a minima). So maybe this:
> 
> "R/qtl is an extension library for the R statistics system.  It is used
> to analyze experimental crosses for identifying genes contributing to
> variation in quantitative traits (so-called quantitative trait loci, QTLs).
> 
> Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
> identify genotyping errors, and to perform single-QTL and two-QTL,
> two-dimensional genome scans."
> 
> (With some inspiration from the fine web site, of course...)
> 
> Andreas
> 

-- 

Re: [PATCH] gnu: Add r-qtl.

[Ludovic Courtès]

Pjotr Prins <pjotr.public12@thebird.nl> skribis:

> I checked with the author and he is fine with your version. 

I think upstream authors shouldn’t be bothered with our own choices of
synopses/descriptions; we have our own context, our own guidelines
etc. that they probably don’t care about.  ;-)

Ludo’.

Re: [PATCH] gnu: Add r-qtl.

[Pjotr Prins]

Well, if he cares, only the better, right? And, actually, I am also
listed as a co-author of this particular software. And I care ;). So
it is a bit more confused than that.

Pj.

On Sun, Sep 20, 2015 at 06:52:19PM +0200, Ludovic Courtès wrote:
> Pjotr Prins <pjotr.public12@thebird.nl> skribis:
> 
> > I checked with the author and he is fine with your version. 
> 
> I think upstream authors shouldn’t be bothered with our own choices of
> synopses/descriptions; we have our own context, our own guidelines
> etc. that they probably don’t care about.  ;-)
> 
> Ludo’.
> 

--