From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add pbtranscript-tofu. Date: Fri, 20 Mar 2015 14:49:15 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:56870) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYxIm-0005Ym-Q2 for guix-devel@gnu.org; Fri, 20 Mar 2015 09:49:30 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YYxIi-0005c5-NO for guix-devel@gnu.org; Fri, 20 Mar 2015 09:49:28 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:47499) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YYxIi-0005bj-9n for guix-devel@gnu.org; Fri, 20 Mar 2015 09:49:24 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 9ED5F380FC7 for ; Fri, 20 Mar 2015 14:49:22 +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 pLLarkzd8uOS for ; Fri, 20 Mar 2015 14:49:16 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 20 Mar 2015 14:49:16 +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@gnu.org --=-=-= Content-Type: text/plain Hi Guix, attached is a patch to add a couple of transcriptome analysis scripts. I had to use the git downloader because the releases are unusable: they are really old and only contain the scripts but no longer the setup.py script. The git clone also isn't that nice; I had to delete some clutter after unpacking and fix the permissions on the python scripts or else installation would fail. About the name: "pbtranscript(-tofu)" is the correct name, whereas "cDNA_primer" is not, even though the repository is named "cDNA_primer". This patch depends on three other packages: - python2-pbcore: http://lists.gnu.org/archive/html/guix-devel/2015-03/msg00573.html - python2-h5py: http://lists.gnu.org/archive/html/guix-devel/2015-03/msg00532.html - python2-bx-python: attached ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-python2-bx-python.patch" >From 39f77a513b2505d2a9658f6f9ed40f24a6b93dfd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Mar 2015 14:39:42 +0100 Subject: [PATCH 1/2] gnu: Add python2-bx-python. * gnu/packages/bioinformatics.scm (python2-bx-python): New variable. --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8592d0..4ab6054 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -289,6 +289,41 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.") (license license:gpl3+))) +(define-public python2-bx-python + (package + (name "python2-bx-python") + (version "0.7.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/b/bx-python/bx-python-" + version ".tar.gz")) + (sha256 + (base32 + "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh")) + (modules '((guix build utils))) + (snippet + '(substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") ""))))) + (build-system python-build-system) + (arguments + `(#:tests? #f ;tests fail because test data are not included + #:python ,python-2)) + (inputs + `(("python-numpy" ,python2-numpy) + ("zlib" ,zlib))) + (native-inputs + `(("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://bitbucket.org/james_taylor/bx-python/") + (synopsis "Tools for manipulating biological data") + (description + "bx-python provides tools for manipulating biological data, particularly +multiple sequence alignments.") + (license license:expat))) + (define-public clipper (package (name "clipper") -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-Add-pbtranscript-tofu.patch" >From 42c865d2c29b7c68e81580de98997266112d6cd9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Mar 2015 14:36:38 +0100 Subject: [PATCH 2/2] gnu: Add pbtranscript-tofu. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable. --- gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4ab6054..46ce4f4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20,6 +20,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system python) @@ -738,6 +739,59 @@ that a read originated from a particular isoform.") files and writing bioinformatics applications.") (license license:bsd-3))) +(define-public pbtranscript-tofu + (package + (name "pbtranscript-tofu") + (version "0.4.1-c7bbd5472") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PacificBiosciences/cDNA_primer.git") + (commit "c7bbd54720df578777743d687ceaf6b4f6d4919e"))) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + ;; With standard flags, the install phase attempts to create a zip'd + ;; egg file, and fails with an error: 'ZIP does not support timestamps + ;; before 1980' + #:configure-flags '("--single-version-externally-managed" + "--record=pbtranscript-tofu.txt") + #:phases + (alist-cons-after + 'unpack 'enter-directory-and-clean-up + (lambda _ + (chdir "pbtranscript-tofu/pbtranscript/") + ;; Delete clutter + (delete-file-recursively "dist/") + (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/") + (delete-file-recursively "pbtools.pbtranscript.egg-info") + (delete-file "Cython-0.20.1.tar.gz") + (delete-file "setuptools_cython-0.2.1-py2.7.egg") + (delete-file "setuptools_cython-0.2.1.tar.gz") + (delete-file "setup.cfg") + ;; files should be writable for install phase + (for-each (lambda (f) (chmod f #o755)) + (find-files "." "\\.py"))) + %standard-phases))) + (inputs + `(("python-cython" ,python2-cython) + ("python-numpy" ,python2-numpy) + ("python-bx-python" ,python2-bx-python) + ("python-pbcore" ,python2-pbcore))) + (native-inputs + `(("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "https://github.com/PacificBiosciences/cDNA_primer") + (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") + (description + "pbtranscript-tofu contains scripts to analyze transcriptome data +generated using the PacBio Iso-Seq protocol.") + (license license:bsd-3))) + (define-public rseqc (package (name "rseqc") -- 2.1.0 --=-=-=--