From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] gnu: Update STAR to 2.5.0c. Date: Tue, 19 Jan 2016 16:29:35 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52371) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aLYE7-0006rm-FL for guix-devel@gnu.org; Tue, 19 Jan 2016 10:29:48 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aLYE3-0000yF-DU for guix-devel@gnu.org; Tue, 19 Jan 2016 10:29:47 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:59417) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aLYE3-0000yA-1J for guix-devel@gnu.org; Tue, 19 Jan 2016 10:29:43 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 38991380F56 for ; Tue, 19 Jan 2016 16:29:42 +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 6Qg3qz8JDm2i for ; Tue, 19 Jan 2016 16:29:35 +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 ; Tue, 19 Jan 2016 16:29:35 +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/x-patch Content-Disposition: inline; filename="0001-gnu-star-Use-modify-phases-syntax.patch" >From e7090b086c71fb8f8a56b6c7cb078b94bc577d2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Jan 2016 16:04:01 +0100 Subject: [PATCH 1/2] gnu: star: Use "modify-phases" syntax. * gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases" syntax. --- gnu/packages/bioinformatics.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 74cadff..d30b0c9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3259,15 +3259,15 @@ of these reads to align data quickly through a hash-based indexing scheme.") '(#:tests? #f ;no check target #:make-flags '("STAR") #:phases - (alist-cons-after - 'unpack 'enter-source-dir (lambda _ (chdir "source")) - (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (install-file "STAR" bin))) - (alist-delete - 'configure %standard-phases))))) + (modify-phases %standard-phases + (add-after 'unpack 'enter-source-dir + (lambda _ (chdir "source") #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (install-file "STAR" bin)) + #t)) + (delete 'configure)))) (native-inputs `(("vim" ,vim))) ; for xxd (inputs -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-star-Update-to-2.5.0c.patch" >From 4efd7a8afe3fbc03f59c1061e9ab2cfcb7c88160 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Jan 2016 16:26:47 +0100 Subject: [PATCH 2/2] gnu: star: Update to 2.5.0c. * gnu/packages/bioinformatics.scm (star): Update to 2.5.0c. [source]: Remove bundled htslib sources and pre-built binaries. [arguments]: Add phase "do-not-use-bundled-htslib". [inputs]: Add "htslib". --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++-------- 1 file changed, 32 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d30b0c9..20a150f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3241,19 +3241,25 @@ of these reads to align data quickly through a hash-based indexing scheme.") (define-public star (package (name "star") - (version "2.4.2a") + (version "2.5.0c") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/alexdobin/STAR/archive/STAR_" - version ".tar.gz")) + (uri (string-append "https://github.com/alexdobin/STAR/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc")) + "1hd662ijwns6rpsd5536sm3h69yfb6xsfkrrrlnyh745gf6d5z4q")) (modules '((guix build utils))) (snippet - '(substitute* "source/Makefile" - (("/bin/rm") "rm"))))) + '(begin + (substitute* "source/Makefile" + (("/bin/rm") "rm")) + ;; Remove pre-built binaries and bundled htslib sources. + (delete-file-recursively "bin/MacOSX_x86_64") + (delete-file-recursively "bin/Linux_x86_64") + (delete-file-recursively "source/htslib") + #t)))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no check target @@ -3262,6 +3268,23 @@ of these reads to align data quickly through a hash-based indexing scheme.") (modify-phases %standard-phases (add-after 'unpack 'enter-source-dir (lambda _ (chdir "source") #t)) + (add-after 'enter-source-dir 'do-not-use-bundled-htslib + (lambda _ + (substitute* "Makefile" + (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" + _ prefix) prefix)) + (substitute* '("BAMfunctions.cpp" + "signalFromBAM.h" + "bam_cat.h" + "bam_cat.c" + "STAR.cpp" + "bamRemoveDuplicates.cpp") + (("#include \"htslib/([^\"]+\\.h)\"" _ header) + (string-append "#include <" header ">"))) + (substitute* "IncludeDefine.h" + (("\"htslib/(htslib/[^\"]+.h)\"" _ header) + (string-append "<" header ">"))) + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) @@ -3271,7 +3294,8 @@ of these reads to align data quickly through a hash-based indexing scheme.") (native-inputs `(("vim" ,vim))) ; for xxd (inputs - `(("zlib" ,zlib))) + `(("htslib" ,htslib) + ("zlib" ,zlib))) (home-page "https://github.com/alexdobin/STAR") (synopsis "Universal RNA-seq aligner") (description -- 2.1.0 --=-=-=--