[PATCH] Update deeptools.

[Ricardo Wurmus]

Hi Guix,

the goal of this series of patches is to update deeptools.

First I moved the “*-pysam” packages from python.scm to
bioinformatics.scm, then updated them.  Then added “pybigwig”, cleaned
up “deeptools” (used “propagated-inputs” for no good reason), and
finally updated the package.

~~ Ricardo

>From f960fda0d38d0a71519072ad8fae8edd7b90b2c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Thu, 25 Feb 2016 14:01:14 +0100
Subject: [PATCH 1/5] gnu: python-pysam, python2-pysam: Move to
 bioinformatics.scm.

* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
  ...here.
---
 gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
 gnu/packages/python.scm         | 38 --------------------------------------
 2 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e570487..a86f7d6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -808,6 +808,44 @@ and more accurate.  BWA-MEM also has better performance 
than BWA-backtrack for
 multiple sequence alignments.")
     (license license:expat)))
 
+(define-public python-pysam
+  (package
+    (name "python-pysam")
+    (version "0.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append 
"https://pypi.python.org/packages/source/p/pysam/pysam-";
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; tests are excluded in the manifest
+       #:phases
+       (alist-cons-before
+        'build 'set-flags
+        (lambda _
+          (setenv "LDFLAGS" "-lncurses")
+          (setenv "CFLAGS" "-D_CURSES_LIB=1"))
+        %standard-phases)))
+    (inputs
+     `(("python-cython"     ,python-cython)
+       ("python-setuptools" ,python-setuptools)
+       ("ncurses"           ,ncurses)
+       ("zlib"              ,zlib)))
+    (home-page "https://github.com/pysam-developers/pysam";)
+    (synopsis "Python bindings to the SAMtools C API")
+    (description
+     "Pysam is a Python module for reading and manipulating files in the
+SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
+also includes an interface for tabix.")
+    (license license:expat)))
+
+(define-public python2-pysam
+  (package-with-python2 python-pysam))
+
 (define-public clipper
   (package
     (name "clipper")
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 46eda76..214a8ea 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1039,44 +1039,6 @@ get the local timezone information, unless you know the 
zoneinfo name, and
 under several distributions that's hard or impossible to figure out.")
     (license cc0)))
 
-(define-public python-pysam
-  (package
-    (name "python-pysam")
-    (version "0.8.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append 
"https://pypi.python.org/packages/source/p/pysam/pysam-";
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; tests are excluded in the manifest
-       #:phases
-       (alist-cons-before
-        'build 'set-flags
-        (lambda _
-          (setenv "LDFLAGS" "-lncurses")
-          (setenv "CFLAGS" "-D_CURSES_LIB=1"))
-        %standard-phases)))
-    (inputs
-     `(("python-cython"     ,python-cython)
-       ("python-setuptools" ,python-setuptools)
-       ("ncurses"           ,ncurses)
-       ("zlib"              ,zlib)))
-    (home-page "https://github.com/pysam-developers/pysam";)
-    (synopsis "Python bindings to the SAMtools C API")
-    (description
-     "Pysam is a Python module for reading and manipulating files in the
-SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
-also includes an interface for tabix.")
-    (license license:expat)))
-
-(define-public python2-pysam
-  (package-with-python2 python-pysam))
-
 (define-public python2-pysqlite
   (package
     (name "python2-pysqlite")
-- 
2.1.0

>From 473a6f8b1e56984b308533a9baa44979c6450e7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Mon, 29 Feb 2016 14:36:25 +0100
Subject: [PATCH 2/5] gnu: python-pysam: Update to 0.8.4.

* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
---
 gnu/packages/bioinformatics.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a86f7d6..28754dc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -811,15 +811,13 @@ multiple sequence alignments.")
 (define-public python-pysam
   (package
     (name "python-pysam")
-    (version "0.8.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append 
"https://pypi.python.org/packages/source/p/pysam/pysam-";
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
+    (version "0.8.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pysam" version))
+              (sha256
+               (base32
+                "1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; tests are excluded in the manifest
-- 
2.1.0

>From 1d58bb0aa9894295f6f949d463bcdfa54b4d2980 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Mon, 29 Feb 2016 14:37:38 +0100
Subject: [PATCH 3/5] gnu: Add python-pybigwig.

* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
  New variables.
---
 gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 28754dc..d7aae6e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1164,6 +1164,47 @@ other types of unwanted sequence from high-throughput 
sequencing reads.")
 files.")
     (license license:expat)))
 
+(define-public python-pybigwig
+  (package
+    (name "python-pybigwig")
+    (version "0.2.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pyBigWig" version))
+              (sha256
+               (base32
+                "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete bundled libBigWig sources
+                  (delete-file-recursively "libBigWig")))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'link-with-libBigWig
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "setup.py"
+               (("libs=\\[") "libs=[\"BigWig\", "))
+             #t)))))
+    (inputs
+     `(("libbigwig" ,libbigwig)
+       ("zlib" ,zlib)
+       ("curl" ,curl)))
+    (home-page "https://github.com/dpryan79/pyBigWig";)
+    (synopsis "Access bigWig files in Python using libBigWig")
+    (description
+     "This package provides Python bindings to the libBigWig library for
+accessing bigWig files.")
+    (license license:expat)))
+
+(define-public python2-pybigwig
+  (let ((pybigwig (package-with-python2 python-pybigwig)))
+    (package (inherit pybigwig)
+      (native-inputs
+       `(("python-setuptools" ,python2-setuptools))))))
+
 (define-public deeptools
   (package
     (name "deeptools")
-- 
2.1.0

>From 37837afefee0df1459322b04b1e26257539b8d02 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Mon, 29 Feb 2016 14:38:57 +0100
Subject: [PATCH 4/5] gnu: deeptools: Change "propagated-inputs" to "inputs".

* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
---
 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 d7aae6e..472219e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1221,7 +1221,7 @@ accessing bigWig files.")
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
-    (propagated-inputs
+    (inputs
      `(("python-scipy" ,python2-scipy)
        ("python-numpy" ,python2-numpy)
        ("python-matplotlib" ,python2-matplotlib)
-- 
2.1.0

>From 197ebd69cc27de3c724d3e01e6c08f843b8b3f07 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Mon, 29 Feb 2016 14:40:10 +0100
Subject: [PATCH 5/5] gnu: deeptools: Update to 2.1.1.

* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
---
 gnu/packages/bioinformatics.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 472219e..6df7d5c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1208,25 +1208,26 @@ accessing bigWig files.")
 (define-public deeptools
   (package
     (name "deeptools")
-    (version "1.5.11")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://github.com/fidelram/deepTools/archive/";
-                    version ".tar.gz"))
+              (uri (string-append "https://github.com/fidelram/deepTools/";
+                                  "archive/" version ".tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1kaagygcbvjs9sxd9cqmskd02wcfp9imvb735r087w7hwqpvz6fs"))))
+                "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
     (inputs
      `(("python-scipy" ,python2-scipy)
        ("python-numpy" ,python2-numpy)
+       ("python-numpydoc" ,python2-numpydoc)
        ("python-matplotlib" ,python2-matplotlib)
        ("python-bx-python" ,python2-bx-python)
-       ("python-pysam" ,python2-pysam)))
+       ("python-pysam" ,python2-pysam)
+       ("python-pybigwig" ,python2-pybigwig)))
     (native-inputs
      `(("python-mock" ,python2-mock) ;for tests
        ("python-pytz" ,python2-pytz) ;for tests
-- 
2.1.0