From patchwork Sat May 18 17:26:34 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 13997 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 4D26F1701E; Sat, 18 May 2019 18:27:08 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 1EF031701E for ; Sat, 18 May 2019 18:27:07 +0100 (BST) Received: from localhost ([127.0.0.1]:36682 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36w-0004G9-OC for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:06 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48557) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36u-0004Dx-Mj for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36t-0001LK-BS for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47619) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36s-0001KX-8V for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36s-0007u2-3z for guix-patches@gnu.org; Sat, 18 May 2019 13:27:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 1/7] gnu: Add tabixpp. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820041430297 (code B ref -1); Sat, 18 May 2019 17:27:02 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:54 +0000 Received: from localhost ([127.0.0.1]:32914 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36j-0007sa-Nt for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:53 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34078) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s8-IF for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:35681) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36a-00018n-QA for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:45 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48421) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D5-BV for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-000161-1T for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:43045) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36X-00014t-RB for guix-patches@gnu.org; Sat, 18 May 2019 13:26:41 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id C9A3A24000E for ; Sat, 18 May 2019 17:26:40 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:34 +0200 Message-Id: <20190518172640.7165-1-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172543.6766-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (tabixpp): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37f2001ea3..244741854d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14830,3 +14830,42 @@ ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, @code{ataqv}, examines aligned reads and reports some basic metrics.") (license license:gpl3+))) + +(define-public tabixpp + (package + (name "tabixpp") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8")))) + (build-system gnu-build-system) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; The build phase needs overriding the location of htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + "HTS_HEADERS=" ; No need to check for headers here. + (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "tabix++" bin))))))) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "C++ wrapper around tabix project") + (description "This is a C++ wrapper around the Tabix project which abstracts +some of the details of opening and jumping in tabix-indexed files.") + (license license:expat))) From patchwork Sat May 18 17:26:35 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 13998 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 A244117027; Sat, 18 May 2019 18:27:08 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 43F5317025 for ; Sat, 18 May 2019 18:27:08 +0100 (BST) Received: from localhost ([127.0.0.1]:36684 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36x-0004H0-Ri for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:07 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48555) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36u-0004Dw-MH for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36t-0001LP-Bm for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47620) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36s-0001Kr-QE for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36s-0007u9-La for guix-patches@gnu.org; Sat, 18 May 2019 13:27:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 2/7] gnu: Add smithwaterman. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820041430305 (code B ref -1); Sat, 18 May 2019 17:27:02 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:54 +0000 Received: from localhost ([127.0.0.1]:32916 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sc-1s for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:54 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34077) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s7-I6 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:32860) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36a-00018Y-H4 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48418) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D4-8u for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-00016G-7N for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:41027) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-000157-10 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 04FEC240011 for ; Sat, 18 May 2019 17:26:40 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:35 +0200 Message-Id: <20190518172640.7165-2-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (smithwaterman): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 244741854d..1bf33853b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14869,3 +14869,33 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (description "This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) + +(define-public smithwaterman + ;; TODO: Upgrading smithwaterman breaks FreeBayes. + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/smithwaterman/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "smithwaterman" bin))))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "Implementation of the Smith-Waterman algorithm.") + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. + (license (list license:gpl2 license:expat))))) From patchwork Sat May 18 17:26:36 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 14002 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 4C13117027; Sat, 18 May 2019 18:27:22 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 3E7D81701E for ; Sat, 18 May 2019 18:27:21 +0100 (BST) Received: from localhost ([127.0.0.1]:36694 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS37A-0004Qj-Mi for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:20 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48571) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36v-0004Dz-5i for guix-patches@gnu.org; Sat, 18 May 2019 13:27:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36t-0001LX-Ce for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47621) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36t-0001LA-9I for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36t-0007uG-3q for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 3/7] gnu: Add multichoose. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820041530319 (code B ref -1); Sat, 18 May 2019 17:27:03 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:55 +0000 Received: from localhost ([127.0.0.1]:32919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sk-ET for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34082) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36h-0007s9-J3 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:47058) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36b-00019L-Eq for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:46 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48434) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36Z-0004D6-Vi for guix-patches@gnu.org; Sat, 18 May 2019 13:26:45 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Y-00016i-Io for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:50409) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015P-8B for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 3633224000A for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:36 +0200 Message-Id: <20190518172640.7165-3-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (multichoose): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1bf33853b0..3ff0f69f5e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14899,3 +14899,39 @@ some of the details of opening and jumping in tabix-indexed files.") (description "Implementation of the Smith-Waterman algorithm.") ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. (license (list license:gpl2 license:expat))))) + +(define-public multichoose + (package + (name "multichoose") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/multichoose/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs")))) + (build-system gnu-build-system) + (native-inputs + `(("python" ,python-2) + ("node" ,node))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + ;; TODO: There are Python modules for these programs too. + (install-file "multichoose" bin) + (install-file "multipermute" bin))))))) + (home-page "https://github.com/ekg/multichoose") + (synopsis "Efficient loopless multiset combination generation algorithm") + (description "This library implements an efficient loopless multiset +combination generation algorithm which is (approximately) described in +\"Loopless algorithms for generating permutations, combinations, and other +combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), +1973. (Algorithm 7.)") + (license license:expat))) From patchwork Sat May 18 17:26:37 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 13999 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 CD68A17027; Sat, 18 May 2019 18:27:09 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 5CE071701E for ; Sat, 18 May 2019 18:27:09 +0100 (BST) Received: from localhost ([127.0.0.1]:36686 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36y-0004Ht-QP for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:08 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48584) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36v-0004FB-Ov for guix-patches@gnu.org; Sat, 18 May 2019 13:27:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36u-0001MJ-9Q for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47622) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36t-0001Lg-MT for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36t-0007uO-J8 for guix-patches@gnu.org; Sat, 18 May 2019 13:27:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 4/7] gnu: Add fsom. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820041930349 (code B ref -1); Sat, 18 May 2019 17:27:03 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:59 +0000 Received: from localhost ([127.0.0.1]:32924 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007tQ-4R for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34111) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sC-AZ for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:44228) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36d-0001B5-L2 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48461) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DN-FU for guix-patches@gnu.org; Sat, 18 May 2019 13:26:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017P-8u for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:58071) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015X-Ih for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 66210240012 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:37 +0200 Message-Id: <20190518172640.7165-4-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (fsom): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ff0f69f5e..e018b51968 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14935,3 +14935,32 @@ combination generation algorithm which is (approximately) described in combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)") (license license:expat))) + +(define-public fsom + (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3")) + (package + (name "fsom") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fsom/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "fsom" bin))))))) + (home-page "https://github.com/ekg/fsom") + (synopsis "Manage SOM (Self-Organizing Maps) neural networks") + (description "A tiny C library for managing SOM (Self-Organizing Maps) +neural networks.") + (license license:gpl3)))) From patchwork Sat May 18 17:26:38 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 14003 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 417ED17027; Sat, 18 May 2019 18:27:32 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 CDB4A1701E for ; Sat, 18 May 2019 18:27:31 +0100 (BST) Received: from localhost ([127.0.0.1]:36698 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS37L-0004Wi-Du for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:31 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48597) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36w-0004GH-G0 for guix-patches@gnu.org; Sat, 18 May 2019 13:27:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36u-0001MT-A4 for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47623) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36u-0001M4-4i for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36u-0007uV-0w for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 5/7] gnu: Add fastahack. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820041930356 (code B ref -1); Sat, 18 May 2019 17:27:03 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:26:59 +0000 Received: from localhost ([127.0.0.1]:32926 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007tS-Fx for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:59 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34112) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sD-Lc for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:49996) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36d-0001BC-QB for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48463) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DO-G4 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017K-8L for guix-patches@gnu.org; Sat, 18 May 2019 13:26:44 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:38251) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Y-00015f-KN for guix-patches@gnu.org; Sat, 18 May 2019 13:26:42 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id 91B17240013 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:38 +0200 Message-Id: <20190518172640.7165-5-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (fastahack): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e018b51968..3ad0a2a421 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14964,3 +14964,35 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), (description "A tiny C library for managing SOM (Self-Organizing Maps) neural networks.") (license license:gpl3)))) + +(define-public fastahack + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) + (package + (name "fastahack") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fastahack/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "fastahack" bin))))))) + (home-page "https://github.com/ekg/fastahack") + (synopsis "Indexing and sequence extraction from FASTA files") + (description "Fastahack is a small application for indexing and +extracting sequences and subsequences from FASTA files. The included library +provides a FASTA reader and indexer that can be embedded into applications +which would benefit from directly reading subsequences from FASTA files. The +library automatically handles index file generation and use.") + (license (list license:expat license:gpl2))))) From patchwork Sat May 18 17:26:39 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 14000 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 DD59A17027; Sat, 18 May 2019 18:27:12 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 1640F1701E for ; Sat, 18 May 2019 18:27:12 +0100 (BST) Received: from localhost ([127.0.0.1]:36688 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS371-0004Ks-Im for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:11 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48598) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36w-0004GI-Gd for guix-patches@gnu.org; Sat, 18 May 2019 13:27:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36u-0001N0-OS for guix-patches@gnu.org; Sat, 18 May 2019 13:27:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47624) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36u-0001Mh-K2 for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36u-0007ud-FG for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 6/7] gnu: Add vcflib. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820042030364 (code B ref -1); Sat, 18 May 2019 17:27:04 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:27:00 +0000 Received: from localhost ([127.0.0.1]:32928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36p-0007ta-Ol for submit@debbugs.gnu.org; Sat, 18 May 2019 13:27:00 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34113) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sE-M2 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:57655) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36e-0001BU-5Q for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48468) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DP-Gk for guix-patches@gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017m-LW for guix-patches@gnu.org; Sat, 18 May 2019 13:26:45 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:35443) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Z-00015x-2e for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id C14E724000F for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:39 +0200 Message-Id: <20190518172640.7165-6-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (vcflib): New variable. --- gnu/packages/bioinformatics.scm | 107 ++++++++++++++++++++++++++++++++ 1 file changed, 107 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ad0a2a421..665c807de9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14870,6 +14870,24 @@ might be caused by ATAC-seq library prep or sequencing. The main program, some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define tabixpp-freebayes + ;; This version works with FreeBayes while the released + ;; version doesn't. The released creates a variable with the name \"vcf\" + ;; somewhere, which is also the name of a namespace in vcflib. + (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) + (package + (inherit tabixpp) + (name "tabixpp-freebayes") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) + (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -14996,3 +15014,92 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) + +(define-public vcflib + (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" )) + (package + (name "vcflib") + (version (git-version "1.0.2" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) + (build-system gnu-build-system) + (native-inputs + `(("zlib" ,zlib) + ;; Submodules. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src.tar.gz") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "fastahack") + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "multichoose-src" "multichoose") + (unpack "smithwaterman-src" "smithwaterman") + (unpack "tabixpp-src" "tabixpp"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("Makefile") + (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "tabixpp" + (invoke "make")) + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + ;; "-I" (assoc-ref inputs "htslib") "/include " + "\"") + "all"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")) + ;; The header files in src/ do not interface libvcflib, + ;; therefore they are left out. + (install-file "libvcflib.a" lib))))))) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) From patchwork Sat May 18 17:26:40 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Pierre Neidhardt X-Patchwork-Id: 14001 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 33AA817027; Sat, 18 May 2019 18:27:18 +0100 (BST) 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,URIBL_BLOCKED autolearn=ham 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 676781701E for ; Sat, 18 May 2019 18:27:17 +0100 (BST) Received: from localhost ([127.0.0.1]:36692 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS376-0004PS-SO for patchwork@mira.cbaines.net; Sat, 18 May 2019 13:27:16 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48601) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36w-0004GX-Qw for guix-patches@gnu.org; Sat, 18 May 2019 13:27:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36v-0001NO-5i for guix-patches@gnu.org; Sat, 18 May 2019 13:27:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47625) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hS36v-0001NG-1j for guix-patches@gnu.org; Sat, 18 May 2019 13:27:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hS36u-0007uk-UL for guix-patches@gnu.org; Sat, 18 May 2019 13:27:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#35792] [PATCH 7/7] gnu: Add freebayes. Resent-From: Pierre Neidhardt Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 18 May 2019 17:27:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 35792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 35792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.155820042030370 (code B ref -1); Sat, 18 May 2019 17:27:04 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2019 17:27:00 +0000 Received: from localhost ([127.0.0.1]:32930 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36q-0007th-68 for submit@debbugs.gnu.org; Sat, 18 May 2019 13:27:00 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34114) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hS36k-0007sF-Mm for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:55 -0400 Received: from lists.gnu.org ([209.51.188.17]:49448) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36e-0001Bb-AH for submit@debbugs.gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from eggs.gnu.org ([209.51.188.92]:48469) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hS36c-0004DQ-Gt for guix-patches@gnu.org; Sat, 18 May 2019 13:26:48 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hS36Z-00017t-P3 for guix-patches@gnu.org; Sat, 18 May 2019 13:26:46 -0400 Received: from relay1-d.mail.gandi.net ([217.70.183.193]:43661) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hS36Z-00016C-6A for guix-patches@gnu.org; Sat, 18 May 2019 13:26:43 -0400 X-Originating-IP: 92.169.116.19 Received: from localhost.localdomain (lfbn-1-4117-19.w92-169.abo.wanadoo.fr [92.169.116.19]) (Authenticated sender: mail@ambrevar.xyz) by relay1-d.mail.gandi.net (Postfix) with ESMTPSA id F2E6F240014 for ; Sat, 18 May 2019 17:26:41 +0000 (UTC) From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:40 +0200 Message-Id: <20190518172640.7165-7-mail@ambrevar.xyz> X-Mailer: git-send-email 2.21.0 In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz> References: <20190518172543.6766-1-mail@ambrevar.xyz> <20190518172640.7165-1-mail@ambrevar.xyz> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x 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 (freebayes): New variable. --- gnu/packages/bioinformatics.scm | 127 ++++++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 665c807de9..704db184eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15103,3 +15103,130 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) + +(define-public freebayes + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") + (revision "1") + (version "1.0.2")) + (package + (name "freebayes") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/freebayes.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("htslib" ,htslib))) + (native-inputs + `(("bc" ,bc) ; Needed for running tests. + ("samtools" ,samtools) ; Needed for running tests. + ("parallel" ,parallel) ; Needed for running tests. + ("procps" ,procps) ; Needed for running tests. + ("bamtools" ,bamtools) + ("bamtools" ,bamtools) + ("vcflib-src" ,(package-source vcflib)) + ;; These are submodules for the vcflib version used in freebayes. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/ekg/intervaltree/archive/" + "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz")) + (file-name "intervaltree-src.tar.gz") + (sha256 + (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks")))) + ;; These submodules are needed to run the tests. + ("bash-tap-src" ,(package-source bash-tap)) + ("test-simple-bash-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ingydotnet/test-simple-bash/") + (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) + (file-name "test-simple-bash-src.tar.gz") + (sha256 + (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) + (arguments + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "vcflib-src" "vcflib") + (unpack "fastahack-src" "vcflib/fastahack") + (unpack "filevercmp-src" "vcflib/filevercmp") + (unpack "fsom-src" "vcflib/fsom") + (unpack "intervaltree-src" "vcflib/intervaltree") + (unpack "multichoose-src" "vcflib/multichoose") + (unpack "smithwaterman-src" "vcflib/smithwaterman") + (unpack "tabixpp-src" "vcflib/tabixpp") + (unpack "test-simple-bash-src" "test/test-simple-bash") + (unpack "bash-tap-src" "test/bash-tap"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "vcflib" + (with-directory-excursion "tabixpp" + (pk "Compile tabixpp before compiling the main project.") + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" "HTS_HEADERS=" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) + (pk "Compile vcflib before compiling the main project.") + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") + "all")) + (pk "Compile the main project.") + (with-directory-excursion "src" + (substitute* "Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) + (invoke "make" + (string-append "BAMTOOLS_ROOT=" + (assoc-ref inputs "bamtools")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "bin/freebayes" bin) + (install-file "bin/bamleftalign" bin)))) + ;; TODO: There are three tests that fail. All because of the -P + ;; (--perl-regexp) option in grep, which is not compiled into the + ;; version of grep in Guix. + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "make" "test"))))))) + (home-page "https://github.com/ekg/freebayes") + (synopsis "Haplotype-based variant detector") + (description "FreeBayes is a Bayesian genetic variant detector designed to +find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), +indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and +complex events (composite insertion and substitution events) smaller than the +length of a short-read sequencing alignment.") + (license license:expat))))