From unknown Sun Jun 15 08:41:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#29532] [PATCH] gnu: Add kallisto. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 Dec 2017 04:19:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 29532 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 29532@debbugs.gnu.org Cc: Ricardo Wurmus X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15121883045982 (code B ref -1); Sat, 02 Dec 2017 04:19:01 +0000 Received: (at submit) by debbugs.gnu.org; 2 Dec 2017 04:18:24 +0000 Received: from localhost ([127.0.0.1]:40850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eKzFw-0001YQ-Dw for submit@debbugs.gnu.org; Fri, 01 Dec 2017 23:18:24 -0500 Received: from eggs.gnu.org ([208.118.235.92]:57391) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eKzFt-0001YB-7Y for submit@debbugs.gnu.org; Fri, 01 Dec 2017 23:18:21 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eKzFm-0000BE-EN for submit@debbugs.gnu.org; Fri, 01 Dec 2017 23:18:15 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.5 required=5.0 tests=BAYES_05,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:52998) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1eKzFm-0000B7-B8 for submit@debbugs.gnu.org; Fri, 01 Dec 2017 23:18:14 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:48344) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1eKzFl-00079x-9B for guix-patches@gnu.org; Fri, 01 Dec 2017 23:18:14 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1eKzFg-00008U-SN for guix-patches@gnu.org; Fri, 01 Dec 2017 23:18:13 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21033) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1eKzFg-000075-Hf for guix-patches@gnu.org; Fri, 01 Dec 2017 23:18:08 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1512131475; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id; l=1735; bh=/redKgXB4Ho7yY17Uja8ATwGr8y4aCYpYnX4TbGPvt4=; b=CzvQxalrqnGh841Ngz0pLXdkKtxxjU16UyL2pBzowUvZ9Kc3I68pru/L+vMp6Cqr Th/m+sKHhMdbYqBEgXm3T7i34yGwb84CpghayYuUFmHnCf7d5y9yGRqJ/DX50eeZW9n tIXrRK53I6Dyq49p1rP2oJ6AsTNigS6NZ6LvEv1M= Received: from localhost (141.80.193.171 [141.80.193.171]) by mx.zohomail.com with SMTPS id 1512131475477764.6816919635011; Fri, 1 Dec 2017 04:31:15 -0800 (PST) From: Ricardo Wurmus Date: Fri, 1 Dec 2017 13:31:14 +0100 Message-Id: <20171201123114.4262-1-rekado@elephly.net> X-Mailer: git-send-email 2.15.0 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [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: -4.0 (----) 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: -4.0 (----) * gnu/packages/bioinformatics.scm (kallisto): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5b3eec86d..f0b589b6c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11079,3 +11079,32 @@ contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data.") ;; GPLv3 only (license license:gpl3))) + +(define-public kallisto + (package + (name "kallisto") + (version "0.43.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pachterlab/" + "kallisto/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; no "check" target + (inputs + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) + (home-page "http://pachterlab.github.io/kallisto/") + (synopsis "Near-optimal RNA-Seq quantification") + (description + "Kallisto is a program for quantifying abundances of transcripts from +RNA-Seq data, or more generally of target sequences using high-throughput +sequencing reads. It is based on the novel idea of pseudoalignment for +rapidly determining the compatibility of reads with targets, without the need +for alignment. Pseudoalignment of reads preserves the key information needed +for quantification, and kallisto is therefore not only fast, but also as +accurate as existing quantification tools.") + (license license:bsd-2))) -- 2.15.0 From debbugs-submit-bounces@debbugs.gnu.org Sun Dec 03 17:18:10 2017 Received: (at control) by debbugs.gnu.org; 3 Dec 2017 22:18:10 +0000 Received: from localhost ([127.0.0.1]:43912 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eLcaQ-000309-2m for submit@debbugs.gnu.org; Sun, 03 Dec 2017 17:18:10 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21025) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1eLcaO-000302-On for control@debbugs.gnu.org; Sun, 03 Dec 2017 17:18:09 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1512339458; s=zoho; d=elephly.net; i=rekado@elephly.net; h=Date:To:From:Subject; l=31; bh=Iza6Ad5U2kd/hKMMPYZLSkW0rPVbijiGB5r5TXdLpwU=; b=RfEEAxgnvAQN9QKC9s9/VtrgAPkSwcoR+ADfGhrLnVOhYQxiN0L5t88x0iHapteU azw9GAI5zJvuw6B7tncGdr6ctNM0/746Y7wAPTjIrGlMV7QjIV41XRFmrN1sttB3ZOT GVCms3F1oan2ilqXNiklSZ4t8ac8ncW7eeplh8fs= Received: from localhost (port-92-200-98-40.dynamic.qsc.de [92.200.98.40]) by mx.zohomail.com with SMTPS id 1512339458876753.988075172351; Sun, 3 Dec 2017 14:17:38 -0800 (PST) Date: Sun, 03 Dec 2017 23:17:36 +0100 To: control@debbugs.gnu.org From: Ricardo Wurmus Subject: control message for bug #29532 X-ZohoMailClient: External X-Spam-Score: 0.1 (/) X-Debbugs-Envelope-To: control 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" Message-Id: X-Spam-Score: -0.0 (/) tags 29532 fixed close 29532