[PATCH] Fixes for MISO.

[PATCH] Fixes for MISO.

[Ricardo Wurmus]

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The current recipe for MISO fails to install the executables.  The first
patch fixes this by patching "setup.py" to use "setuptools" rather than
"distutils.core".  It also adds new native inputs, because these
executables require testing.

The second patch changes the protocol of the tarball URL from http to
https; pypi redirects to https.

~~ Ricardo


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From b8c6ece9d658969a0ce8054e368df96ce293c30f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 17 Jun 2015 12:14:39 +0200
Subject: [PATCH 1/2] gnu: miso: Install executables.

* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
  "setuptools" so that executables are built.
* gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
  and "python2-pytz".
---
 gnu/packages/bioinformatics.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4a55040..30bc581 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1301,9 +1301,12 @@ sequencing tag position and orientation.")
                (base32
                 "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
               (modules '((guix build utils)))
-              ;; use "gcc" instead of "cc" for compilation
               (snippet
                '(substitute* "setup.py"
+                  ;; Use setuptools, or else the executables are not
+                  ;; installed.
+                  (("distutils.core") "setuptools")
+                  ;; use "gcc" instead of "cc" for compilation
                   (("^defines")
                    "cc.set_executables(
 compiler='gcc',
@@ -1321,7 +1324,9 @@ linker_so='gcc -shared'); defines")))))
        ("python-scipy" ,python2-scipy)
        ("python-matplotlib" ,python2-matplotlib)))
     (native-inputs
-     `(("python-setuptools" ,python2-setuptools)))
+     `(("python-mock" ,python2-mock) ;for tests
+       ("python-pytz" ,python2-pytz) ;for tests
+       ("python-setuptools" ,python2-setuptools)))
     (home-page "http://genes.mit.edu/burgelab/miso/index.html")
     (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
     (description
-- 
2.1.0


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From 062066c95d8dca286feb063f544f20a686b00d7e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 17 Jun 2015 12:16:40 +0200
Subject: [PATCH 2/2] gnu: miso: Use HTTPS URL.

* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
  downloading the source tarball.
---
 gnu/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 30bc581..e43021d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1295,7 +1295,7 @@ sequencing tag position and orientation.")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://pypi.python.org/packages/source/m/misopy/misopy-"
+                    "https://pypi.python.org/packages/source/m/misopy/misopy-"
                     version ".tar.gz"))
               (sha256
                (base32
-- 
2.1.0

Re: [PATCH] Fixes for MISO.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From b8c6ece9d658969a0ce8054e368df96ce293c30f Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 17 Jun 2015 12:14:39 +0200
> Subject: [PATCH 1/2] gnu: miso: Install executables.
>
> * gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
>   "setuptools" so that executables are built.
> * gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
>   and "python2-pytz".

OK.

> From 062066c95d8dca286feb063f544f20a686b00d7e Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 17 Jun 2015 12:16:40 +0200
> Subject: [PATCH 2/2] gnu: miso: Use HTTPS URL.
>
> * gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
>   downloading the source tarball.

OK.

Don’t hesitate to push non-controversial changes like these after a
couple of days have passed.

Thanks!

Ludo’.

Re: [PATCH] Fixes for MISO.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> Don’t hesitate to push non-controversial changes like these after a
> couple of days have passed.

Thank you, I'll do that.

~~ Ricardo