[PATCH] Add express-beta-diversity

[PATCH] Add express-beta-diversity

[Ben Woodcroft]

[-- Attachment #1: Type: text/plain, Size: 459 bytes --]

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

[-- Attachment #2: 0001-gnu-Add-express-beta-diversity.patch --]
[-- Type: text/x-patch, Size: 2825 bytes --]

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

Re: [PATCH] Add express-beta-diversity

[Andreas Enge]

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

Re: [PATCH] Add express-beta-diversity

[Ludovic Courtès]

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’.

Re: [PATCH] Add express-beta-diversity

[Benjamin Woodcroft]

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’.