From patchwork Thu Dec 5 21:21:14 2019 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: 16393 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 F38DF17851; Thu, 5 Dec 2019 21:22:11 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id ABBAC1784F for ; Thu, 5 Dec 2019 21:22:11 +0000 (GMT) Received: from localhost ([::1]:32786 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icyZf-00022T-2K for patchwork@mira.cbaines.net; Thu, 05 Dec 2019 16:22:11 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:40448) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icyZY-0001wV-1a for guix-patches@gnu.org; Thu, 05 Dec 2019 16:22:05 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1icyZW-0008CZ-Kj for guix-patches@gnu.org; Thu, 05 Dec 2019 16:22:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:39398) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1icyZW-0008BP-AE for guix-patches@gnu.org; Thu, 05 Dec 2019 16:22:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1icyZW-0000Uc-5b for guix-patches@gnu.org; Thu, 05 Dec 2019 16:22:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#38505] [PATCH] gnu: Add fast-screen. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 05 Dec 2019 21:22:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 38505 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 38505@debbugs.gnu.org Cc: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.15755809131874 (code B ref -1); Thu, 05 Dec 2019 21:22:01 +0000 Received: (at submit) by debbugs.gnu.org; 5 Dec 2019 21:21:53 +0000 Received: from localhost ([127.0.0.1]:45371 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1icyZM-0000UA-H1 for submit@debbugs.gnu.org; Thu, 05 Dec 2019 16:21:52 -0500 Received: from lists.gnu.org ([209.51.188.17]:44590) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1icyZK-0000U2-F7 for submit@debbugs.gnu.org; Thu, 05 Dec 2019 16:21:51 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:37981) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1icyZI-0001vM-M9 for guix-patches@gnu.org; Thu, 05 Dec 2019 16:21:50 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1icyZH-0007Hz-07 for guix-patches@gnu.org; Thu, 05 Dec 2019 16:21:48 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:38023) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1icyZE-0006Zc-DM for guix-patches@gnu.org; Thu, 05 Dec 2019 16:21:46 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id EF451160078 for ; Thu, 5 Dec 2019 22:21:26 +0100 (CET) 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; s= mdc; t=1575580886; x=1577395287; bh=UPiMOdzDGIwlrxQWinca59EiKQvj dn7UxHR6CItWx2g=; b=LYeQowZ48RP2rtvKUYOUh9hmtF1ROmBfe5rHjND1fkEW u5P+CiyasqlziBvCoytLtoYOJjE3ABUWBMsrfrLuic2FKgD6H6ojKzIpX1Q0Mhwq epGZMQv+EF8ApRf6bX5Ndc0+dKy0JWYkeZ/r69dE0aSVpmaCsG7oe07IJAN2cmM= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 6022YY4-COi4 for ; Thu, 5 Dec 2019 22:21:26 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Thu, 5 Dec 2019 22:21:26 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Thu, 5 Dec 2019 22:21:25 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 5 Dec 2019 22:21:14 +0100 Message-ID: <20191205212114.4971-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25086.003 X-TM-AS-Result: No-2.671700-8.000000-10 X-TMASE-MatchedRID: WRg89AGrPJHOHeyV0sB3ziiAdOasssq5Ww/S0HB7eoMHZBaLwEXlKJYz hAg0ec5DYb5ngTAod3Cb6AP/cW2Tplx2G18wlcS+ihCjnGX2dsQjFTUmyJTlsfv7ndOc2uMkzKh I/PM+wq/QqxdHfo1SKqf2Uzyi/W3Pgq5omviqSMrB6S7ffS3eaxHgf7O7X8hvIFBEE5CFomJGcK Gl2h7b3aXSz2BM3j41PX/M4l4Wq1iRS8vMCpHzH8PRlYRmv+e2QxituV8iXjv4/8apt2/jKF+1W WNdGyeDZl9pgrxXl3HO/nM50i6/ArQBD8Gbrcz9SyH6bNPVSds4m0JsW63IXN9zZd3pUn7K4twQ ekPJIH3zYSR0cBhKIOzznoLIx35HIX2cSk+kRR9JUdgxNDUXWp2kkHiPIXr9VwFyHlDMkdPNHy8 Ow4dZrtEmLPmPRz4ZitMvRrEqw5GjxYyRBa/qJV/Hpl/zcOjl6WhiDOOieuzKayT/BQTiGnXgXs Qkv1481AD+eiPgtEKW1cGkIDwvpeudLcHzuXyD+R15Dzi8A9WnbyDd0C0JErYL4U3FHUcSS51+k uoBcJtL/mGFueGs/DGSmMlbsu5xXyZ6pl/oDQ1+Az0rNWZh1oK3xHwHujePaS3XXfcxpZY= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.671700-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25086.003 X-TM-SNTS-SMTP: 07DF9C19CA04A3DCF6FE25BE0E2D600F057D4BE07AD5A59689EDC56C3B25A2352000:9 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (fast-screen): New variable. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 74a44874ee..53e4c7296f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15341,3 +15341,56 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public fastq-screen + (package + (name "fastq-screen") + (version "0.14.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.bioinformatics.babraham.ac.uk/projects/" + "fastq_screen/fastq_screen_v" version ".tar.gz")) + (sha256 + (base32 + "0m7n9b1pr8rk1pd3va0mr69pd7gddcsvrvlk2s7907i02wkc1say")))) + (build-system trivial-build-system) + (arguments + ;; it is just an extraction processs + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((tar (assoc-ref %build-inputs "tar")) + (gzip (assoc-ref %build-inputs "gzip")) + (out (assoc-ref %outputs "out")) + (doc (string-append out "/share/doc")) + (bin (string-append out "/bin"))) + (setenv "PATH" (string-append tar "/bin:" gzip "/bin")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) + (chdir (string-append "fastq_screen_v" ,version)) + (install-file "fastq_screen" bin) + (install-file "fastq_screen.conf.example" doc) + (install-file "fastq_screen_documentation.md" doc) + (install-file "RELEASE_NOTES.txt" doc) + #t)))) + (inputs + `(("perl" ,perl))) + (native-inputs + `(("gzip" ,gzip) + ("tar" ,tar))) + (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/") + (synopsis "FastQ Screen allows to search a large sequence dataset") + (description + "FastQ Screen is an application which allows you to search a large sequence +dataset against a panel of different databases to build up a picture of where +the sequences in your data originate. The program was built as a quality +control check for sequencing pipelines but may also have uses in metagenomics +studies where mixed samples are expected. The application generates both text +and graphical output to inform you what proportion of your library was able to +map, either uniquely or to more than one location, against each of your +specified reference genomes. The user should therefore be able to identify a +clean sequencing experiment in which the overwhelming majority of reads are +probably derived from a single genomic origin.") + (license license:gpl3+))) +