From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Update deeptools. Date: Mon, 29 Feb 2016 14:47:04 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57851) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aaOAO-0006Es-TS for guix-devel@gnu.org; Mon, 29 Feb 2016 08:47:18 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aaOAL-0001Eg-FN for guix-devel@gnu.org; Mon, 29 Feb 2016 08:47:16 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:44359) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aaOAK-0001EY-U2 for guix-devel@gnu.org; Mon, 29 Feb 2016 08:47:13 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 66936380E28 for ; Mon, 29 Feb 2016 14:47:11 +0100 (CET) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id kHtFFMKwkzxV for ; Mon, 29 Feb 2016 14:47:05 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Mon, 29 Feb 2016 14:47:05 +0100 (CET) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel --=-=-= Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Guix, the goal of this series of patches is to update deeptools. First I moved the =E2=80=9C*-pysam=E2=80=9D packages from python.scm to bioinformatics.scm, then updated them. Then added =E2=80=9Cpybigwig=E2=80= =9D, cleaned up =E2=80=9Cdeeptools=E2=80=9D (used =E2=80=9Cpropagated-inputs=E2=80=9D = for no good reason), and finally updated the package. ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-python-pysam-python2-pysam-Move-to-bioinformatic.patch" >From f960fda0d38d0a71519072ad8fae8edd7b90b2c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus 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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-python-pysam-Update-to-0.8.4.patch" >From 473a6f8b1e56984b308533a9baa44979c6450e7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus 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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0003-gnu-Add-python-pybigwig.patch" >From 1d58bb0aa9894295f6f949d463bcdfa54b4d2980 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus 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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0004-gnu-deeptools-Change-propagated-inputs-to-inputs.patch" >From 37837afefee0df1459322b04b1e26257539b8d02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus 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 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0005-gnu-deeptools-Update-to-2.1.1.patch" >From 197ebd69cc27de3c724d3e01e6c08f843b8b3f07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus 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 --=-=-=--