From mboxrd@z Thu Jan 1 00:00:00 1970 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 Subject: [bug#38505] [PATCH] gnu: Add fast-screen. Resent-Message-ID: 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) 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) From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Thu, 5 Dec 2019 22:21:14 +0100 Message-ID: <20191205212114.4971-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 38505@debbugs.gnu.org Cc: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= * 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+))) + -- 2.17.1