From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Update deeptools.
Date: Mon, 29 Feb 2016 14:47:04 +0100 [thread overview]
Message-ID: <idjegbv1vdz.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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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
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From f960fda0d38d0a71519072ad8fae8edd7b90b2c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
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[-- Attachment #3: 0002-gnu-python-pysam-Update-to-0.8.4.patch --]
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From 473a6f8b1e56984b308533a9baa44979c6450e7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
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[-- Attachment #4: 0003-gnu-Add-python-pybigwig.patch --]
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From 1d58bb0aa9894295f6f949d463bcdfa54b4d2980 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
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From 37837afefee0df1459322b04b1e26257539b8d02 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
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From 197ebd69cc27de3c724d3e01e6c08f843b8b3f07 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
next reply other threads:[~2016-02-29 13:47 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-02-29 13:47 Ricardo Wurmus [this message]
2016-03-03 1:50 ` [PATCH] Update deeptools Leo Famulari
2016-03-03 12:32 ` Ricardo Wurmus
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