From unknown Wed Jun 18 23:10:20 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#31667 <31667@debbugs.gnu.org> To: bug#31667 <31667@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add minimap2. Reply-To: bug#31667 <31667@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:10:20 +0000 retitle 31667 [PATCH] gnu: Add minimap2. reassign 31667 guix-patches submitter 31667 Ricardo Wurmus severity 31667 normal tag 31667 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Thu May 31 09:45:07 2018 Received: (at submit) by debbugs.gnu.org; 31 May 2018 13:45:07 +0000 Received: from localhost ([127.0.0.1]:55722 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fONt0-0004QP-Hq for submit@debbugs.gnu.org; Thu, 31 May 2018 09:45:07 -0400 Received: from eggs.gnu.org ([208.118.235.92]:41398) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fONsw-0004Pc-7O for submit@debbugs.gnu.org; Thu, 31 May 2018 09:44:59 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fONsp-0001Sk-SI for submit@debbugs.gnu.org; Thu, 31 May 2018 09:44:53 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:38368) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fONsp-0001SW-Ov for submit@debbugs.gnu.org; Thu, 31 May 2018 09:44:51 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:60598) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fONso-0006x9-EQ for guix-patches@gnu.org; Thu, 31 May 2018 09:44:51 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fONsj-0001IR-Ho for guix-patches@gnu.org; Thu, 31 May 2018 09:44:50 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:60544) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fONsj-0001D0-66 for guix-patches@gnu.org; Thu, 31 May 2018 09:44:45 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 1888411627B5 for ; Thu, 31 May 2018 15:44:42 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:x-mailer:message-id:date :date:subject:subject:from:from:received:received:received :received; s=mdc; t=1527774275; x=1529588676; bh=BfZR9c0A0GHeDLs kQYoeyPkXPbvd/QekFSa/LnADZWQ=; b=FH+1/64h3wGm00KitpfFkXXeqSKmnHn kS3Z1CviX94NvBJwCrTGaUAI9SrekhNjxvhLCsaO6XvWaHqNMe3LHZ8RZN3Cookj YlQ4cvMZ52RMxb8WCyu7D+0Ljj7L8q4HdXw18gTrWwJn5qizMO+Ls1/HxgOQfw8N zrJB0/+zoahE= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id II0oHaJRay7x for ; Thu, 31 May 2018 15:44:35 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Thu, 31 May 2018 15:44:35 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) by HTCATWO.mdc-berlin.net (141.80.180.190) with Microsoft SMTP Server (TLS) id 14.3.399.0; Thu, 31 May 2018 15:44:35 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Thu, 31 May 2018 15:44:34 +0200 From: Ricardo Wurmus To: Subject: [PATCH] gnu: Add minimap2. Date: Thu, 31 May 2018 15:44:23 +0200 Message-ID: <20180531134423.15286-1-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.16.3 MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.2.1013-23878.006 X-TM-AS-Result: No-0.084400-8.000000-10 X-TMASE-MatchedRID: H2wTq3MMruh7qToVEfwBPAPZZctd3P4BwLlnHU0okA2YGQ7Y8LLoS8XP WWL1fCKxelcgeWORKyrAzwwNvqF4zkhrEQpQtQpn/jkwiY2tJnKeW/QqOEIboxHfiujuTbedVto y0Ca8CITlbhztVRDw3c/yPGhtlTCiKyG2Dpa679pxfk94zHLa/m5N71UY7eq8IFBEE5CFomIkGj 8hicui0DrOLGHGdU6d1CWy6B4rx1HE+/p97o4OwLMjW/sniEQKB4Id7CiQcz8slIt0blYHr+DGe ai2z4nO4vM1YF6AJbbCCfuIMF6xLaxZXRt2R/g50zEewRngEgtdKdvF1RgqLwz9ehnQ34kG7VtF OvmD/8ehaCMUI4d5j/J0WJuaxh0tWbJZx+BDxsUtvY9OLyn4KIAIJiERUMCdp5JjyxdFJbmH+Jd 1tLVXu7uPatbFhAu3RwaeWU9Z9+E3XT7h8Le0wID1CQ7wlvFu X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.084400-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.2.1013-23878.006 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) * gnu/packages/bioinformatics.scm (minimap2): New variable. --- gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index abea91372..26b135ef7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13185,3 +13185,62 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) + +(define-public minimap2 + (package + (name "minimap2") + (version "2.10") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/lh3/minimap2/" + "releases/download/v" version "/" + "minimap2-" version ".tar.bz2")) + (sha256 + (base32 + "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:make-flags + (list "CC=gcc" + (let ((system ,(or (%current-target-system) + (%current-system)))) + (cond + ((string-prefix? "x86_64" system) + "all") + ((or (string-prefix? "armhf" system) + (string-prefix? "aarch64" system)) + "arm_neon=1") + (_ "sse2only=1")))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (install-file "minimap2" bin) + (mkdir-p man) + (install-file "minimap2.1" man)) + #t))))) + (inputs + `(("zlib" ,zlib))) + (home-page "Pairwise aligner for genomic and spliced nucleotide sequences") + (synopsis "https://lh3.github.io/minimap2/") + (description "Minimap2 is a versatile sequence alignment program that +aligns DNA or mRNA sequences against a large reference database. Typical use +cases include: + +@enumerate +@item mapping PacBio or Oxford Nanopore genomic reads to the human genome; +@item finding overlaps between long reads with error rate up to ~15%; +@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA + reads against a reference genome; +@item aligning Illumina single- or paired-end reads; +@item assembly-to-assembly alignment; +@item full-genome alignment between two closely related species with + divergence below ~15%. +@end enumerate\n") + (license license:expat))) -- 2.16.3 From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 14 07:53:44 2018 Received: (at 31667-done) by debbugs.gnu.org; 14 Jun 2018 11:53:44 +0000 Received: from localhost ([127.0.0.1]:47382 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fTQoy-0007iJ-Lv for submit@debbugs.gnu.org; Thu, 14 Jun 2018 07:53:44 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:41208) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fTQow-0007iB-Oh for 31667-done@debbugs.gnu.org; Thu, 14 Jun 2018 07:53:43 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id C644D11903D8 for <31667-done@debbugs.gnu.org>; Thu, 14 Jun 2018 13:53:41 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :subject:subject:from:from:user-agent:received:received:received :received; s=mdc; t=1528977216; x=1530791617; bh=tTel+YpqNNRBq9K CfVzXL9OCatZ7r0TFywAMyxYW7Ik=; b=pjVB4YmybMsrmYemIG1/YOUTcAa25an IpoWVQJcoRxTy6OarCNIor94SXQbCV1VRk4bOMmaxejj3cCV6LDfn7ndKUgQv/e4 bdLa1SwwEep+9uycMWlZxphyLhjL5OJ5fhCfCupQC2dJO5NerHhp3BoeUkWNIW3L iihuA7WIhx1I= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id J2XHwgpFnNl5 for <31667-done@debbugs.gnu.org>; Thu, 14 Jun 2018 13:53:36 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <31667-done@debbugs.gnu.org>; Thu, 14 Jun 2018 13:53:36 +0200 (CEST) Received: from SW-IT-P-CAS2.mdc-berlin.net (141.80.113.54) by HTCAONE.mdc-berlin.net (141.80.180.120) with Microsoft SMTP Server (TLS) id 14.3.399.0; Thu, 14 Jun 2018 13:53:35 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS2.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server id 14.3.399.0; Thu, 14 Jun 2018 13:53:34 +0200 User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: <31667-done@debbugs.gnu.org> Subject: [PATCH] gnu: Add minimap2. 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