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[82.242.148.1]) by smtp.gmail.com with ESMTPSA id y70sm4574993wmc.36.2020.05.02.06.48.27 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 06:48:28 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 15:48:15 +0200 Message-Id: <20200502134815.13390-3-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502134815.13390-1-vincent.legoll@gmail.com> References: <20200502134815.13390-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 X-Spam-Score: 4.09 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=qirPi9/R; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 2001:470:142::17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Scan-Result: default: False [4.09 / 13.00]; RCVD_VIA_SMTP_AUTH(0.00)[]; GENERIC_REPUTATION(0.00)[-0.49501571252965]; TO_DN_SOME(0.00)[]; R_SPF_ALLOW(-0.20)[+ip6:2001:470:142::/48:c]; R_DKIM_REJECT(1.00)[gmail.com:s=20161025]; DWL_DNSWL_FAIL(0.00)[2001:470:142::17:server fail]; FREEMAIL_FROM(0.00)[gmail.com]; BROKEN_CONTENT_TYPE(1.50)[]; R_MISSING_CHARSET(2.50)[]; IP_REPUTATION_HAM(0.00)[asn: 22989(0.15), country: US(-0.00), ip: 2001:470:142::17(-0.50)]; DKIM_TRACE(0.00)[gmail.com:-]; RCPT_COUNT_TWO(0.00)[2]; MX_GOOD(-0.50)[cached: eggs.gnu.org]; MAILLIST(-0.20)[mailman]; FORGED_RECIPIENTS_MAILLIST(0.00)[]; RCVD_IN_DNSWL_FAIL(0.00)[2001:470:142::17:server fail]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_LAST(0.00)[]; ASN(0.00)[asn:22989, ipnet:2001:470:142::/48, country:US]; TAGGED_FROM(0.00)[larch=yhetil.org]; ARC_NA(0.00)[]; FROM_NEQ_ENVFROM(0.00)[vincentlegoll@gmail.com,guix-patches-bounces@gnu.org]; FROM_HAS_DN(0.00)[]; URIBL_BLOCKED(0.00)[gromacs.org:url]; MID_RHS_MATCH_FROM(0.00)[]; TAGGED_RCPT(0.00)[]; PREVIOUSLY_DELIVERED(0.00)[40691@debbugs.gnu.org]; MIME_GOOD(-0.10)[text/plain]; HAS_LIST_UNSUB(-0.01)[]; FREEMAIL_CC(0.00)[gmail.com]; RCVD_COUNT_SEVEN(0.00)[10]; FORGED_SENDER_MAILLIST(0.00)[]; DMARC_POLICY_SOFTFAIL(0.10)[gmail.com : SPF not aligned (relaxed),none] X-TUID: HlphXzTYHMws * 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 02eae3b589..0727d1bac8 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_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") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("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)); + } -- 2.26.0