* [PATCH] Add express-beta-diversity
@ 2015-10-15 13:11 Ben Woodcroft
2015-10-15 20:39 ` Andreas Enge
2015-11-02 8:57 ` Ludovic Courtès
0 siblings, 2 replies; 4+ messages in thread
From: Ben Woodcroft @ 2015-10-15 13:11 UTC (permalink / raw
To: guix-devel@gnu.org, Donovan Parks
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Hi,
I noticed when packaging this that when "python" is provided as an input
(and not python-2), then the python scripts don't get their shebangs
fixed, because there is no python executable in the $PATH (it is
python3). This seems not right to me - is there a reason for this, maybe
so python 2 and 3 can coexist?
In this case the python script was written with python-2 in mind so it
doesn't matter here though. Thanks in advance for the review.
ben
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From 8d6f94c67df09e7830414fcf748da311a1167314 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 15 Oct 2015 22:53:31 +1000
Subject: [PATCH] gnu: Add express-beta-diversity.
* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4b7f76b..8c2cbb1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1086,6 +1086,51 @@ analysis (from RNA-Seq), transcription factor binding quantification in
ChIP-Seq, and analysis of metagenomic data.")
(license license:artistic2.0)))
+(define-public express-beta-diversity
+ (package
+ (name "express-beta-diversity")
+ (version "1.0.7")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
+ (replace 'check
+ (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
+ "-u"))))
+ (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-file "scripts/convertToEBD.py"
+ (string-append bin "/convertToEBD.py"))
+ (copy-file "bin/ExpressBetaDiversity"
+ (string-append bin "/ExpressBetaDiversity"))
+ #t))))))
+ (inputs
+ `(("python" ,python-2)))
+ (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
+ (synopsis "Taxon- and phylogenetic-based beta diversity measures")
+ (description
+ "Express Beta Diversity (EBD) calculates ecological beta diversity
+(dissimilarity) measures between biological communities. EBD implements a
+variety of diversity measures including those that make use of phylogenetic
+similarity of community members.")
+ (license license:gpl3+)))
+
(define-public fasttree
(package
(name "fasttree")
--
2.4.3
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] Add express-beta-diversity
2015-10-15 13:11 [PATCH] Add express-beta-diversity Ben Woodcroft
@ 2015-10-15 20:39 ` Andreas Enge
2015-11-02 8:57 ` Ludovic Courtès
1 sibling, 0 replies; 4+ messages in thread
From: Andreas Enge @ 2015-10-15 20:39 UTC (permalink / raw
To: Ben Woodcroft; +Cc: guix-devel@gnu.org, Donovan Parks
On Thu, Oct 15, 2015 at 11:11:39PM +1000, Ben Woodcroft wrote:
> I noticed when packaging this that when "python" is provided as an input
> (and not python-2), then the python scripts don't get their shebangs fixed,
> because there is no python executable in the $PATH (it is python3). This
> seems not right to me - is there a reason for this, maybe so python 2 and 3
> can coexist?
Yes. Our python package follows upstream and only provides binaries called
python3 and python3.4. The python-2.7.10 package also follows upstream
(you can see a pattern here :-)) and provides python, python2 and python2.7.
You will probably want to use python-wrapper, which corresponds to the
python package with an additional symbolic link python->python3
(and some others); it is actually used in a number of package recipes.
Andreas
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] Add express-beta-diversity
2015-10-15 13:11 [PATCH] Add express-beta-diversity Ben Woodcroft
2015-10-15 20:39 ` Andreas Enge
@ 2015-11-02 8:57 ` Ludovic Courtès
2015-11-02 14:51 ` Benjamin Woodcroft
1 sibling, 1 reply; 4+ messages in thread
From: Ludovic Courtès @ 2015-11-02 8:57 UTC (permalink / raw
To: Ben Woodcroft; +Cc: guix-devel@gnu.org, Donovan Parks
Hi Ben,
It seems this one had fallen through the cracks, sorry about that!
Don’t hesitate to ping if that happens in the future.
Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:
> I noticed when packaging this that when "python" is provided as an
> input (and not python-2), then the python scripts don't get their
> shebangs fixed, because there is no python executable in the $PATH (it
> is python3). This seems not right to me - is there a reason for this,
> maybe so python 2 and 3 can coexist?
By default Python 3.x only installs a ‘python3’ command. There’s a
‘python-wrapper’ package to provide a ‘python’ wrapper for ‘python3’.
> From 8d6f94c67df09e7830414fcf748da311a1167314 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Thu, 15 Oct 2015 22:53:31 +1000
> Subject: [PATCH] gnu: Add express-beta-diversity.
>
> * gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Pushed. Thanks, and apologies for the delay!
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] Add express-beta-diversity
2015-11-02 8:57 ` Ludovic Courtès
@ 2015-11-02 14:51 ` Benjamin Woodcroft
0 siblings, 0 replies; 4+ messages in thread
From: Benjamin Woodcroft @ 2015-11-02 14:51 UTC (permalink / raw
To: Ludovic Courtès; +Cc: guix-devel@gnu.org, Donovan Parks
No problems, I'm on holidays anyway. Thanks.
________________________________________
From: Ludovic Courtès <ludo@gnu.org>
Sent: Monday, November 2, 2015 6:57 PM
To: Benjamin Woodcroft
Cc: guix-devel@gnu.org; Donovan Parks
Subject: Re: [PATCH] Add express-beta-diversity
Hi Ben,
It seems this one had fallen through the cracks, sorry about that!
Don’t hesitate to ping if that happens in the future.
Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:
> I noticed when packaging this that when "python" is provided as an
> input (and not python-2), then the python scripts don't get their
> shebangs fixed, because there is no python executable in the $PATH (it
> is python3). This seems not right to me - is there a reason for this,
> maybe so python 2 and 3 can coexist?
By default Python 3.x only installs a ‘python3’ command. There’s a
‘python-wrapper’ package to provide a ‘python’ wrapper for ‘python3’.
> From 8d6f94c67df09e7830414fcf748da311a1167314 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Thu, 15 Oct 2015 22:53:31 +1000
> Subject: [PATCH] gnu: Add express-beta-diversity.
>
> * gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Pushed. Thanks, and apologies for the delay!
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
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2015-10-15 13:11 [PATCH] Add express-beta-diversity Ben Woodcroft
2015-10-15 20:39 ` Andreas Enge
2015-11-02 8:57 ` Ludovic Courtès
2015-11-02 14:51 ` Benjamin Woodcroft
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