From patchwork Fri Feb 23 09:11:49 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 60910 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 28E4727BBEA; Fri, 23 Feb 2024 10:05:18 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E29F427BBE2 for ; Fri, 23 Feb 2024 10:05:16 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rdSQ6-000282-4I; Fri, 23 Feb 2024 05:04:42 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rdSQ3-00027A-Fg for guix-patches@gnu.org; Fri, 23 Feb 2024 05:04:39 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rdSQ3-0005bv-63 for guix-patches@gnu.org; Fri, 23 Feb 2024 05:04:39 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rdSQQ-00031c-GF; Fri, 23 Feb 2024 05:05:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#69322] [PATCH] gnu: Add trust4. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 23 Feb 2024 10:05:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 69322 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69322@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.170868268011547 (code B ref -1); Fri, 23 Feb 2024 10:05:02 +0000 Received: (at submit) by debbugs.gnu.org; 23 Feb 2024 10:04:40 +0000 Received: from localhost ([127.0.0.1]:56064 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rdSQ3-00030B-PA for submit@debbugs.gnu.org; Fri, 23 Feb 2024 05:04:40 -0500 Received: from lists.gnu.org ([209.51.188.17]:55844) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rdSPz-0002z9-J2 for submit@debbugs.gnu.org; Fri, 23 Feb 2024 05:04:37 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rdRca-00044F-My for guix-patches@gnu.org; Fri, 23 Feb 2024 04:13:32 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rdRcY-0005CY-6U for guix-patches@gnu.org; Fri, 23 Feb 2024 04:13:32 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1708679592; x=1710493993; bh=06YCJYyMOnzaHpM 1k9fogtn2HhUC4R6/bA4Mxlhjns0=; b=mfs4VTHJ4b5ZIPz36GlTvzw2PAe6O7P /0FEKRIQVskiaMW/Y1E91L2Toiu7oyc7w8jkAx6M37qE/SqAkLIVzmna1tGBbN22 4UEMmznYxrjlJ84dNHl5h/Ha/+RkCwTfvefpIh+1QAvX0lpfK50JTMTpFm2MGmxp FNqzNiN3aDvE= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 463111601AD for ; Fri, 23 Feb 2024 10:13:11 +0100 (CET) Received: from cl-akalin11.mdc-berlin.net (141.80.219.20) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.2.1544.4; Fri, 23 Feb 2024 10:13:10 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 23 Feb 2024 10:11:49 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Originating-IP: [141.80.219.20] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.1006-28208.006 X-TM-AS-Result: No-10--3.380500-5.000000 X-TMASE-MatchedRID: O+K0RiZ4x2p6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqWqypIpj8HBpype4ofkluPsa87CDXaKRVILwteD+QnyUBHfiujuTbedT+q 8D2QRzgeQ8jX9l2qhLQFIAkrbeDHfeFTBDh9n8Ezece0aRiX9WkaYLapw9QQ+7nmyqxTSZEU5d9 n04fLNZvZ34hI7tEmHA4LlpTxyt9+0+ZONdwr5U7nHu4BcYSmtMoS2PLq1B76A+SHJ+g3ONpmWG EaoO8rlcMsQvHf7bJuOH4cxOFNFrY/nMJGIbnlE4nbwqqmOd2lZDdHiTk9OcIq1ysJFea53lIOV A+gJRdKI0Ejneva935soi2XrUn/JUTdY/mdfTXtJKW4mDlJsMcK21zBg2Klfoubv1b7BWh3ZN4q d2FSKjwo4FMXRmu844PEkBl4n178QrSDDHtmomIGqGZSXenDoLbWR5eXywiLuHUT1v5wk3JfnNK psD1+YBWaxsMwYx/IoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.380500-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28208.006 X-TM-SNTS-SMTP: 02CCAC949A717078D95BC0877402617AF4C152747B17B6C528165794CDC22ADD2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches gnu/packages/bioinformatics.scm (trust4): New variable. Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf --- gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) base-commit: 5f86eebd240958001ab4f178005f355d24d9b7f1 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 554df0b42f..06aad16982 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5552,6 +5552,82 @@ (define-public repeat-masker bases are detected.") (license license:osl2.1))) +(define-public trust4 + (package + (name "trust4") + (version "1.0.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/liulab-dfci/TRUST4") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "058wd5bklgcsb0r8l7n1ffakbj4c3ac5hjyvmaqhr3p233fl44z7")) + (modules '((guix build utils))) + (snippet '(begin + ;; Remove bundled samtools + (delete-file-recursively "samtools-0.1.19"))))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;there are no tests + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-samtools-headers + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile" + (("LINKPATH= -I./samtools-0.1.19 -L./samtools-0.1.19") + (string-append "LINKPATH= -I." + #$(this-package-native-input "samtools") + "/include/samtools" + " -L." + #$(this-package-native-input "samtools") + "/lib")) + (("./samtools-0.1.19/") + (string-append #$(this-package-native-input + "samtools") "/lib/"))) + (substitute* "alignments.hpp" + (("samtools-0.1.19") + (string-append #$(this-package-native-input + "samtools") "/include/samtools"))))) + (delete 'configure) ; No configure. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (scripts (string-append #$output + "/share/trust4/scripts"))) + (install-file "annotator" bin) + (install-file "bam-extractor" bin) + (install-file "fastq-extractor" bin) + (install-file "run-trust4" bin) + (install-file "trust4" bin) + ;; install scripts stored in the scrips dir + (for-each (lambda (file) + (chmod file #o555)) + (find-files "scripts" "\\.p(y|l)")) + (copy-recursively "scripts" scripts) + (delete-file-recursively "scripts") + ;; install the rest of the scripts that are in the main dir + (for-each (lambda (file) + (chmod file #o555) + (install-file file bin)) + (find-files "." "\\.(pl|py|sh)")))))))) + (native-inputs (list automake samtools-0.1)) + (inputs (list perl python-wrapper zlib)) + (home-page "https://github.com/liulab-dfci/TRUST4") + (synopsis "TCR and BCR assembly from RNA-seq data") + (description "This package is analyzing @acronym{TCR, T cell receptor} and +@acronym{BCR, B cell receptor} sequences using unselected RNA sequencing data, +profiled from fluid and solid tissues, including tumors. TRUST4 performs de +novo assembly on V, J, C genes including the hypervariable @acronym{CDR3, +complementarity-determining region 3} and reports consensus contigs of BCR/TCR +sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to +identify the corresponding gene and CDR3 details. TRUST4 supports both single-end +and paired-end bulk or single-cell sequencing data with any read length.") + (license license:gpl3))) + (define-public diamond (package (name "diamond")