From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add FASTX Toolkit. Date: Tue, 14 Apr 2015 16:39:57 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36742) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Yi20b-00080N-93 for guix-devel@gnu.org; Tue, 14 Apr 2015 10:40:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Yi20U-0003bH-W2 for guix-devel@gnu.org; Tue, 14 Apr 2015 10:40:13 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:37593) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Yi20U-0003WD-Jn for guix-devel@gnu.org; Tue, 14 Apr 2015 10:40:06 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id D7EF5280671 for ; Tue, 14 Apr 2015 16:40:04 +0200 (CEST) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 76VaZzw7NX1Q for ; Tue, 14 Apr 2015 16:39:58 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Tue, 14 Apr 2015 16:39:58 +0200 (CEST) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Guix-devel --=-=-= Content-Type: text/plain Hi Guix, attached are patches to add fastx-toolkit, and its dependency libgtextutils. "fastx-toolkit" installs three m4 files to "$out/share/aclocal", and libgtextutils installs an empty "$out/share/aclocal" directoy. I reported this upstream, but I did not add a phase to remove these files, because I think it's not a big deal. Is this okay or should I modify the sources to avoid installing these files? ~~ Ricardo --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-libgtextutils.patch" >From 673f316fd41b0d0d7679a7a69ed4755923873653 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 14 Apr 2015 16:35:30 +0200 Subject: [PATCH 1/2] gnu: Add libgtextutils. * gnu/packages/textutils.scm (libgtextutils): New variable. --- gnu/packages/textutils.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index d6cc577..2f367ce 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -23,6 +23,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) + #:use-module (gnu packages autotools) #:use-module (gnu packages python)) (define-public recode @@ -122,3 +123,33 @@ libenca and several charset conversion libraries and tools.") normalization, case-folding, and other operations for data in the UTF-8 encoding, supporting Unicode version 7.0.") (license license:expat))) + +(define-public libgtextutils + (package + (name "libgtextutils") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/agordon/libgtextutils/releases/download/" + version "/libgtextutils-" version ".tar.gz")) + (sha256 + (base32 "0jiybkb2z58wa2msvllnphr4js2hvjvh988pavb3mzkgr6ihwbkr")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (alist-cons-after + 'unpack 'autoreconf + (lambda _ (zero? (system* "autoreconf" "-vif"))) + %standard-phases))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (home-page "http://hannonlab.cshl.edu/fastx_toolkit") + (synopsis "Gordon's text utils library") + (description + "libgtextutils is a text utilities library used by the fastx toolkit from +the Hannon Lab.") + (license license:agpl3+))) -- 2.1.0 --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0002-gnu-Add-FASTX-Toolkit.patch" >From 1d386b93064eb839e0156938ac38919daa654839 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 14 Apr 2015 16:36:30 +0200 Subject: [PATCH 2/2] gnu: Add FASTX Toolkit. * gnu/packages/bioinformatics.scm (fastx-toolkit): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 615d70d..0239e97 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages swig) #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) #:use-module (gnu packages vim) #:use-module (gnu packages xml) #:use-module (gnu packages zip)) @@ -473,6 +474,38 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public fastx-toolkit + (package + (name "fastx-toolkit") + (version "0.0.14") + (source (origin + (method url-fetch) + (uri + (string-append + "https://github.com/agordon/fastx_toolkit/releases/download/" + version "/fastx_toolkit-" version ".tar.bz2")) + (sha256 + (base32 + "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) + (build-system gnu-build-system) + (inputs + `(("libgtextutils" ,libgtextutils))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") + (synopsis "Tools for FASTA/FASTQ file preprocessing") + (description + "The FASTX-Toolkit is a collection of command line tools for Short-Reads +FASTA/FASTQ files preprocessing. + +Next-Generation sequencing machines usually produce FASTA or FASTQ files, +containing multiple short-reads sequences. The main processing of such +FASTA/FASTQ files is mapping the sequences to reference genomes. However, it +is sometimes more productive to preprocess the files before mapping the +sequences to the genome---manipulating the sequences to produce better mapping +results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") + (license license:agpl3+))) + (define-public flexbar (package (name "flexbar") -- 2.1.0 --=-=-=--