From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add preseq. Date: Tue, 23 Jun 2015 13:02:43 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33862) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z7Lyl-0002Bd-1A for guix-devel@gnu.org; Tue, 23 Jun 2015 07:03:02 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z7Lyf-0004vl-M6 for guix-devel@gnu.org; Tue, 23 Jun 2015 07:02:58 -0400 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:45708) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z7Lyf-0004ti-9m for guix-devel@gnu.org; Tue, 23 Jun 2015 07:02:53 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 6C379280995 for ; Tue, 23 Jun 2015 13:02:50 +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 bRzAaqJKxY_3 for ; Tue, 23 Jun 2015 13:02:43 +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, 23 Jun 2015 13:02:43 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-preseq.patch" 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 >From 7e0352fad776f1c491882647ee3ad5f5319e1164 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 23 Jun 2015 10:54:00 +0200 Subject: [PATCH] gnu: Add preseq. * gnu/packages/bioinformatics.scm (preseq): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09534a8..3d36120 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2004,6 +2004,57 @@ Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.") (license license:public-domain))) +(define-public preseq + (package + (name "preseq") + (version "1.0.2") + (source (origin + (method url-fetch) + (uri + (string-append "http://smithlabresearch.org/downloads/preseq-" + version ".tar.bz2")) + (sha256 + (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc")) + (modules '((guix build utils))) + (snippet + ;; Remove bundled samtools. + ;; FIXME: Without samtools sources "bam2mr" is not built. + '(delete-file-recursively "preseq-master/samtools")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-after + 'unpack 'enter-dir + (lambda _ + (chdir "preseq-master") + #t)) + (replace 'configure + (lambda* (#:key inputs #:allow-other-keys) + ;; Fix install target + (substitute* "Makefile" + (("\\$\\(ROOT\\)/bin") "$(PREFIX)/bin")) + #t))) + #:make-flags (list (string-append "PREFIX=" + (assoc-ref %outputs "out")) + ;; Do not attempt to link samtools objects + "SAMTOOLS_DIR="))) + (inputs + `(("gsl" ,gsl) + ("zlib" ,zlib))) + (home-page "http://smithlabresearch.org/software/preseq/") + (synopsis "Program for analyzing library complexity") + (description + "The preseq package is aimed at predicting and estimating the complexity +of a genomic sequencing library, equivalent to predicting and estimating the +number of redundant reads from a given sequencing depth and how many will be +expected from additional sequencing using an initial sequencing experiment. +The estimates can then be used to examine the utility of further sequencing, +optimize the sequencing depth, or to screen multiple libraries to avoid low +complexity samples.") + (license license:gpl3+))) + (define-public sra-tools (package (name "sra-tools") -- 2.1.0