From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] gnu: Add bedtools Date: Mon, 15 Dec 2014 16:46:13 +0100 Message-ID: References: <87fvckyrrg.fsf@netris.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:47183) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Y0Xqx-0002Dj-Vd for guix-devel@gnu.org; Mon, 15 Dec 2014 10:46:37 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Y0Xqp-0006Yf-1h for guix-devel@gnu.org; Mon, 15 Dec 2014 10:46:31 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:45379) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Y0Xqo-0006X4-MA for guix-devel@gnu.org; Mon, 15 Dec 2014 10:46:22 -0500 In-Reply-To: <87fvckyrrg.fsf@netris.org> 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: Mark H Weaver Cc: guix-devel@gnu.org --=-=-= Content-Type: text/plain Thanks for the review and the suggestions. Attached is an updated patch for bedtools. Python has been marked as a native input as it is only required at build time to run a script that creates shell script wrappers for the various executables. I hope that's correct. --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-bedtools.patch" >From 5d1d383417992369e6fa3f81331e87471183ffc6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Dec 2014 17:37:16 +0100 Subject: [PATCH] gnu: Add bedtools * gnu/packages/bioinformatics.scm (bedtools): New variable. --- gnu/packages/bioinformatics.scm | 49 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f6178a..d608a34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -28,6 +28,55 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python)) +(define-public bedtools + (package + (name "bedtools") + (version "2.22.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl")))) + (build-system gnu-build-system) + (native-inputs `(("python" ,python-2))) + (inputs `(("samtools" ,samtools) + ("zlib" ,zlib))) + (arguments + '(#:test-target "test" + #:phases + (alist-cons-after + 'unpack 'patch-makefile-SHELL-definition + (lambda _ + ;; patch-makefile-SHELL cannot be used here as it does not + ;; yet patch definitions with `:='. Since changes to + ;; patch-makefile-SHELL result in a full rebuild, features + ;; of patch-makefile-SHELL are reimplemented here. + (substitute* "Makefile" + (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n")))) + (alist-delete + 'configure + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (for-each (lambda (file) + (copy-file file (string-append bin (basename file)))) + (find-files "bin" ".*")))) + %standard-phases))))) + (home-page "https://github.com/arq5x/bedtools2") + (synopsis "Swiss army knife for genome arithmetic") + (description + "Collectively, the bedtools utilities are a swiss-army knife of tools for +a wide-range of genomics analysis tasks. The most widely-used tools enable +genome arithmetic: that is, set theory on the genome. For example, bedtools +allows one to intersect, merge, count, complement, and shuffle genomic +intervals from multiple files in widely-used genomic file formats such as BAM, +BED, GFF/GTF, VCF.") + (license license:gpl2))) + (define-public samtools (package (name "samtools") -- 1.9.3 --=-=-=--