From patchwork Sat May 2 16:43:23 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Vincent Legoll X-Patchwork-Id: 21844 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 2AFD727BBE4; Sat, 2 May 2020 17:45:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:470:142::17]) by mira.cbaines.net (Postfix) with ESMTP id DBE9527BBE1 for ; Sat, 2 May 2020 17:45:10 +0100 (BST) Received: from localhost ([::1]:45396 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jUvGI-0006cG-Db for patchwork@mira.cbaines.net; Sat, 02 May 2020 12:45:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53470) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jUvGA-0006Zw-Sy for guix-patches@gnu.org; Sat, 02 May 2020 12:45:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jUvGA-000487-3H for guix-patches@gnu.org; Sat, 02 May 2020 12:45:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42226) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jUvG9-00046E-MW for guix-patches@gnu.org; Sat, 02 May 2020 12:45:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jUvG9-000643-Ie for guix-patches@gnu.org; Sat, 02 May 2020 12:45:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 1/3] gnu: Add tng. References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 16:45:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158843784423197 (code B ref 40691); Sat, 02 May 2020 16:45:01 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 16:44:04 +0000 Received: from localhost ([127.0.0.1]:53768 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEx-000616-Us for submit@debbugs.gnu.org; Sat, 02 May 2020 12:44:04 -0400 Received: from mail-wr1-f67.google.com ([209.85.221.67]:42586) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEv-00060o-UG for 40691@debbugs.gnu.org; Sat, 02 May 2020 12:43:46 -0400 Received: by mail-wr1-f67.google.com with SMTP id s8so5296895wrt.9 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 09:43:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=y8nTGttrET5Hj7hEfv7HvRf4qZBPZFFmK88eZ/2pfF4=; b=p7ZEjsa4kCWctSZhifLvFLiGWNJzxiJZlBhdqgExLMVpBtrd3ockvHEfPmUNyCdutw n/dXD9zYKPqGPXSCwt5Z5zviQUx6jMCEgLaZZVHBthuqjuoyEkOVMWfc6gAUOVc3CBw/ k3+xl7dydSndc32E0Vxq2R46qX8A9Ja2j6iGDboKsV3rkiSpSebyt1LHtzP9iVixLAXp ceWabneuCCX/NMiy8haSFRbToaWpkHR7afX9dOFF6FdhkUsVSLBLf8BVYAPiIjeyZZyu TXNU299NdhfjnyhQr1hHuEJbEPv4DN5XOIi/PpnYKZKpI8UwnWZsLc10WyCRKclKlErG ftBw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=y8nTGttrET5Hj7hEfv7HvRf4qZBPZFFmK88eZ/2pfF4=; b=WcNKLS9SuEX0ponRWUqXxsLBasMeaPH4WPGM1Iq9ZFVqxE/b+a1BNI8OfjPzqp9Jgt aaaxQaxpFUrttpH/wKoAX9sPifnfB6wa11LSYn6V89bv5VM9aCsfSyP+i09x21agR88z c0Rus7NjACo7tJkC+k7Mfv0oXIaGNsRfN2qhKEdOPSH2teST4X0Lo5s3r4+angwcgJGq aElCeCnsGRW6/4yqhjXT7oYaHB09sR6FL/r04QeG2lToL3fSwWvu2SJG+xApo9OLb3OD vUAsEUavAbOYf6S1x7FY7cpGydMABnEotE8O02RdXjLwY8G83nI9pMsY5jfZ9mQjppSf du5w== X-Gm-Message-State: AGi0PuZqggQP2Y7ZBy/iYkzC9wTp8iqTNul27VQGZwKl6Z4Yz646+RAl wpIi1E6FUQVsvQ8IwTjHkxRZJsrD X-Google-Smtp-Source: APiQypKMFasEqKPSIkMaSKlt46K6kK+TGKW7/T3lkIYUU9Gr3wWcOsqO5VklkeMg5JzF2GX1UBfb9g== X-Received: by 2002:adf:f884:: with SMTP id u4mr9781585wrp.171.1588437819660; Sat, 02 May 2020 09:43:39 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q17sm4841598wmj.45.2020.05.02.09.43.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 09:43:39 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 18:43:23 +0200 Message-Id: <20200502164325.2028-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 (tng): 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 65b44568e0..f90401a560 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -785,6 +786,41 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public tng + (package + (name "tng") + (version "1.8.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gromacs/tng.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) + (build-system cmake-build-system) + (inputs + `(("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-bundled-zlib + (lambda _ + (delete-file-recursively "external") + #t)) + (replace 'check + (lambda _ + (invoke "../build/bin/tests/tng_testing") + #t))))) + (home-page "https://github.com/gromacs/tng") + (synopsis "Trajectory Next Generation binary format manipulation library") + (description "TRAJNG (Trajectory next generation) is a program library for +handling molecular dynamics (MD) trajectories. It can store coordinates, and +optionally velocities and the H-matrix. Coordinates and velocities are +stored with user-specified precision.") + (license license:bsd-3))) + (define-public python-pybedtools (package (name "python-pybedtools") From patchwork Sat May 2 16:43:24 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vincent Legoll X-Patchwork-Id: 21845 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 7793227BBE4; Sat, 2 May 2020 17:45:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:470:142::17]) by mira.cbaines.net (Postfix) with ESMTP id 305BB27BBE1 for ; Sat, 2 May 2020 17:45:11 +0100 (BST) Received: from localhost ([::1]:45398 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jUvGI-0006cQ-NK for patchwork@mira.cbaines.net; Sat, 02 May 2020 12:45:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53476) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jUvGB-0006Zx-4Q for guix-patches@gnu.org; Sat, 02 May 2020 12:45:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jUvGA-0004AD-F9 for guix-patches@gnu.org; Sat, 02 May 2020 12:45:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42227) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jUvGA-00048X-1J for guix-patches@gnu.org; Sat, 02 May 2020 12:45:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jUvG9-00064E-V3 for guix-patches@gnu.org; Sat, 02 May 2020 12:45:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 2/3] gnu: Add lmfit. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 16:45:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158843784523204 (code B ref 40691); Sat, 02 May 2020 16:45:01 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 16:44:05 +0000 Received: from localhost ([127.0.0.1]:53770 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvFE-000626-S6 for submit@debbugs.gnu.org; Sat, 02 May 2020 12:44:05 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:43607) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEw-00060q-DF for 40691@debbugs.gnu.org; Sat, 02 May 2020 12:43:50 -0400 Received: by mail-wr1-f42.google.com with SMTP id i10so15577247wrv.10 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 09:43:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=OyUC+rWNb3RlHyyRtTx3Ii3iDXR9s6Pnu73y0PTM+0k=; b=UKHFasx69UmOY+lpo2m9KDxTLHwk1keP5suG0Vuau9h6rWduBRU12NDnFZBPJUptJE kbAz0cYGg3JlSUiSMPa6t67n/f+0fkzHW3wEQ0BkyfM6GbeT7VXnT4g+0B9j2M92oNGq DFDr2zh4GmxLPHq0evZ6l23t6opNDjkj2LwF/KhG3LvbWOmh+yzT41wO6+KK96H3h7r0 m25R3ClAYcSU3jmPFnExui7Wt21Jp1fX+HVFt6GMUYNCS0J9ryaU5AWIgVS5L1+g1s2R fhQnQpe0HHYcXSRwNSoroU/CcIry+hx/x1S2qQVZzW7DapjTvdyiEOoASTTw43wpbw4s hFLw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=OyUC+rWNb3RlHyyRtTx3Ii3iDXR9s6Pnu73y0PTM+0k=; b=kb+SJ4PD/CWHy4Wy8Qwq5Bul9x4of39gpcWfr9vuFuzUJ1UMg7cbjEVakkoINZHZ0v WCzqmqAfg9rES9PZ5Bqh2VzA6W6km2LBoU4vbwCu6IHosCRpR3Ujryxm5nMbY3cLCWK1 ORfx5NnK+BzD3jQWQu/IBb6l9/EiOrRt2szskerlG3qZ2Xgz5m5SgpsGoZFYhSpDvTn0 GjEhhL9WsfhgE/F8Y1hU7/fIC7v7x1hE8Z30LwuPlQIC1HEefLE65K09jT0iz1xAKPI0 Tnhu4bnptgakwKhO2ng47fhCwncdyZwDx8cOld6l+Uj1/lvapMrmJiPycgBBPnoCbTLq zzzA== X-Gm-Message-State: AGi0Puayhpgn+YbNfSEnJz1EKa47jnw/Lni1F38zd3+jXyz9Pe7WUA2C E9e720fTEmXvb+aAT7xFExmQh6HG X-Google-Smtp-Source: APiQypLagxBQyeTY5HQIcZL1w4guItWe0WyEBa0SYbeyEFmNedRgM8VI6eBVVfCIWjhePvjWGSPc2w== X-Received: by 2002:adf:cd12:: with SMTP id w18mr5981872wrm.341.1588437820537; Sat, 02 May 2020 09:43:40 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q17sm4841598wmj.45.2020.05.02.09.43.39 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 09:43:40 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 18:43:24 +0200 Message-Id: <20200502164325.2028-2-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502164325.2028-1-vincent.legoll@gmail.com> References: <20200502164325.2028-1-vincent.legoll@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 (lmfit): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f90401a560..1e3e145500 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -821,6 +821,30 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public lmfit + (package + (name "lmfit") + (version "8.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://jugit.fz-juelich.de/mlz/lmfit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf")))) + (build-system cmake-build-system) + (native-inputs + `(("perl" ,perl))) ; for pod2man + (home-page "https://jugit.fz-juelich.de/mlz/lmfit") + (synopsis "C library for Levenberg-Marquardt minimization and least-squares +fitting") + (description "lmfit is a C library for Levenberg-Marquardt least-squares +minimization and curve fitting. It is mature code, based on decades-old +algorithms from the FORTRAN library MINPACK.") + (license license:bsd-2))) + (define-public python-pybedtools (package (name "python-pybedtools") From patchwork Sat May 2 16:43:25 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vincent Legoll X-Patchwork-Id: 21846 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 D2C1627BBE4; Sat, 2 May 2020 17:45:17 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:470:142::17]) by mira.cbaines.net (Postfix) with ESMTP id 2F85827BBE1 for ; Sat, 2 May 2020 17:45:17 +0100 (BST) Received: from localhost ([::1]:45764 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jUvGO-0006vm-PC for patchwork@mira.cbaines.net; Sat, 02 May 2020 12:45:16 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53496) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jUvGD-0006dh-CS for guix-patches@gnu.org; Sat, 02 May 2020 12:45:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jUvGA-0004CK-Rr for guix-patches@gnu.org; Sat, 02 May 2020 12:45:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42228) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jUvGA-0004Ae-Dn for guix-patches@gnu.org; Sat, 02 May 2020 12:45:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jUvGA-00064L-BH for guix-patches@gnu.org; Sat, 02 May 2020 12:45:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 3/3] gnu: Add gromacs. 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[82.242.148.1]) by smtp.gmail.com with ESMTPSA id q17sm4841598wmj.45.2020.05.02.09.43.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 09:43:41 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 18:43:25 +0200 Message-Id: <20200502164325.2028-3-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502164325.2028-1-vincent.legoll@gmail.com> References: <20200502164325.2028-1-vincent.legoll@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++ gnu/packages/patches/gromacs-tinyxml2.patch | 50 ++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 gnu/packages/patches/gromacs-tinyxml2.patch diff --git a/gnu/local.mk b/gnu/local.mk index 812253b192..70e8879284 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1004,6 +1004,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e3e145500..13d9c16c10 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -80,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -845,6 +846,89 @@ minimization and curve fitting. It is mature code, based on decades-old algorithms from the FORTRAN library MINPACK.") (license license:bsd-2))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + (patches (search-patches "gromacs-tinyxml2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ; The following has been submitted upstream + (substitute* "src/testutils/CMakeLists.txt" + (("target_link_libraries\\(testutils \\$") + "target_link_libraries(testutils PRIVATE $")) + ; Unbundling +; (delete-file-recursively "src/external/vmd_molfile") + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") +; (delete-file-recursively "src/external/thread_mpi") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..3dace595d2 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,50 @@ +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + }