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Date: Fri, 23 Feb 2024 10:11:49 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain 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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -2.4 (--) gnu/packages/bioinformatics.scm (trust4): New variable. Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf --- gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) 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") base-commit: 5f86eebd240958001ab4f178005f355d24d9b7f1 -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon May 06 06:52:25 2024 Received: (at 69322-done) by debbugs.gnu.org; 6 May 2024 10:52:25 +0000 Received: from localhost ([127.0.0.1]:37221 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3vxJ-00084Z-1a for submit@debbugs.gnu.org; Mon, 06 May 2024 06:52:25 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21184) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3vxG-00084S-Le for 69322-done@debbugs.gnu.org; Mon, 06 May 2024 06:52:23 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1714992716; cv=none; d=zohomail.com; s=zohoarc; b=QJyC1mVHwa+7w5NYi7IJz9+QHA/tb6DFM+4nGk5IfOcJ+gmSK28wniMxC4mpIEgUtRiCbFZTjW1mJuMP8NRUMmA1mcyCnaH9dvOCxYf9GS6RmDrO2dbtIh5Q6gIU8IibMfOEA8PpZ2KXuek3JG8sM1ESWNMUUgC/BhuWrsgLIlE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1714992716; h=Content-Type:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=WSveNLlob1bbDNwrWlGn34MKTP3ANU7ZS1F74XMY9lM=; b=h9QEKCRV8UYsqh3X3tI1Dp+Kc/jkW0r2WsocMVqFq1cPeRoFVUVEgTYQ+nWr1GZWi+OpUO/FyqtgC4jK8+Cbt4TdWb9NanHhDQNlLjYkYchQhoXLy1lqzGzgMvad6tOTc/AAZUho8xPDSPIXTWYafKPwkeYbLYq+fuAV+DViXI4= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1714992716; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:In-Reply-To:References:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=WSveNLlob1bbDNwrWlGn34MKTP3ANU7ZS1F74XMY9lM=; b=XCzG8C/JTc2Bb/f0amltSdIQYlp8/2bgwRO8UGoQi+AHPXGjEdwFQgoJivj2wrYg 0B5IYrp6sEhiWYQcte1G4iIQGcLa38nnuwHw7y71mLAR4yoyGoEsNIlWi67QkKOR9/b SXdhpz6dnPzfIKmIf9JdJAnr/3d2ivNwQ7m/Dffw= Received: by mx.zohomail.com with SMTPS id 1714992712665868.0144557879088; Mon, 6 May 2024 03:51:52 -0700 (PDT) From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#69322] [PATCH] gnu: Add trust4. In-Reply-To: (=?utf-8?B?Ik3Eg2TEg2xpbg==?= Ionel =?utf-8?Q?Patra=C8=99cu=22's?= message of "Fri, 23 Feb 2024 10:11:49 +0100") References: User-Agent: mu4e 1.12.4; emacs 29.3 Date: Mon, 06 May 2024 12:51:48 +0200 Message-ID: <8734qvkybf.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 69322-done Cc: 69322-done@debbugs.gnu.org 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: -1.0 (-) > gnu/packages/bioinformatics.scm (trust4): New variable. My apologies for the delay. This email fell through the cracks. I've pushed this now and followed it up with an update to the package. -- Ricardo From unknown Fri Jul 18 08:21:57 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Mon, 03 Jun 2024 11:24:09 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator