diff options
Diffstat (limited to 'gnu/packages/chemistry.scm')
| -rw-r--r-- | gnu/packages/chemistry.scm | 95 |
1 files changed, 42 insertions, 53 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d2ad632d2c..94803719ac 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -70,20 +70,20 @@ (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("eigen" ,eigen) - ("mmtf-cpp" ,mmtf-cpp) - ("msgpack" ,msgpack) - ("googletest" ,googletest) - ("pkg-config" ,pkg-config) - ("pybind11" ,pybind11))) + (list eigen + mmtf-cpp + msgpack + googletest + pkg-config + pybind11)) (inputs - `(("glew" ,glew) - ("libarchive" ,libarchive) - ("libmsym" ,libmsym) - ("molequeue" ,molequeue) - ("python" ,python) - ("spglib" ,spglib) - ("qtbase" ,qtbase-5))) + (list glew + libarchive + libmsym + molequeue + python + spglib + qtbase-5)) (arguments '(#:configure-flags (list "-DENABLE_TESTING=ON" (string-append "-DSPGLIB_INCLUDE_DIR=" @@ -113,13 +113,9 @@ bioinformatics, materials science, and related areas.") (file-name (git-file-name name version)))) (build-system cmake-build-system) (native-inputs - `(("eigen" ,eigen) - ("pkg-config" ,pkg-config))) + (list eigen pkg-config)) (inputs - `(("avogadrolibs" ,avogadrolibs) - ("hdf5" ,hdf5) - ("molequeue" ,molequeue) - ("qtbase" ,qtbase-5))) + (list avogadrolibs hdf5 molequeue qtbase-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments '(#:tests? #f)) @@ -147,7 +143,7 @@ powerful plugin architecture.") "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr")))) (build-system python-build-system) (inputs - `(("python-mmtk" ,python2-mmtk))) + (list python2-mmtk)) (arguments `(#:python ,python-2 ;; No test suite @@ -195,8 +191,7 @@ only with Python 2 and NumPy < 1.9.") (include-dir (string-append out "/include/inchi")) (lib (string-append out "/lib/inchi")) (inchi-doc (assoc-ref inputs "inchi-doc")) - (unzip (string-append (assoc-ref inputs "unzip") - "/bin/unzip"))) + (unzip (search-input-file inputs "/bin/unzip"))) (chdir "../../..") ;; Install binary. (with-directory-excursion "INCHI_EXE/bin/Linux" @@ -304,7 +299,7 @@ biological structures.") "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998")))) (build-system cmake-build-system) (inputs - `(("qtbase" ,qtbase-5))) + (list qtbase-5)) (arguments '(#:configure-flags '("-DENABLE_TESTING=ON") #:phases @@ -356,12 +351,10 @@ staged, and output files collected using a standard interface.") "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r")))) (build-system python-build-system) (inputs - `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib)) - ("python-scientific" ,python2-scientific) - ("netcdf" ,netcdf) - ("gv" ,gv))) + (list (with-numpy-1.8 python2-matplotlib) python2-scientific netcdf + gv)) (propagated-inputs - `(("python-mmtk" ,python2-mmtk))) + (list python2-mmtk)) (arguments `(#:python ,python-2 #:tests? #f ; No test suite @@ -417,7 +410,7 @@ NumPy < 1.9.") "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) (build-system cmake-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (arguments `(#:phases (modify-phases %standard-phases @@ -503,13 +496,13 @@ stored with user-specified precision.") ("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))) + (list fftwf + `(,hwloc-2 "lib") + lmfit + openblas + perl + tinyxml2 + tng)) (home-page "http://www.gromacs.org/") (synopsis "Molecular dynamics software package") (description "GROMACS is a versatile package to perform molecular dynamics, @@ -550,12 +543,9 @@ usual algorithms you expect from a modern molecular dynamics implementation.") (assoc-ref %build-inputs "inchi") "/include/inchi")) #:test-target "test")) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("eigen" ,eigen) - ("inchi" ,inchi) - ("libxml2" ,libxml2) - ("zlib" ,zlib))) + (list eigen inchi libxml2 zlib)) (home-page "http://openbabel.org/wiki/Main_Page") (synopsis "Chemistry data manipulation toolbox") (description @@ -650,19 +640,18 @@ symmetries written in C. Spglib can be used to: (string-append "--prefix=" (assoc-ref outputs "out")) "--root=/")))))) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("freeglut" ,freeglut) - ("glew" ,glew) - ("libxml2" ,libxml2) - ("mmtf-cpp" ,mmtf-cpp) - ("msgpack" ,msgpack) - ("python-pyqt" ,python-pyqt) - ("glm" ,glm) - ("netcdf" ,netcdf))) + (list freetype + libpng + freeglut + glew + libxml2 + mmtf-cpp + msgpack + python-pyqt + glm + netcdf)) (native-inputs - `(("catch2" ,catch-framework2) - ("python-setuptools" ,python-setuptools))) + (list catch-framework2 python-setuptools)) (home-page "https://pymol.org") (synopsis "Molecular visualization system") (description "PyMOL is a capable molecular viewer and renderer. It can be |