diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 71 |
1 files changed, 71 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e7b99ee61..01718426ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -161,6 +161,7 @@ #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages uglifyjs) + #:use-module (gnu packages video) #:use-module (gnu packages vim) #:use-module (gnu packages web) #:use-module (gnu packages wget) @@ -4287,6 +4288,76 @@ annotations of the genome.") other types of unwanted sequence from high-throughput sequencing reads.") (license license:expat))) +(define-public lammps + (let ((commit "stable_2Aug2023_update2")) + (package + (name "lammps") + (version (string-append "0." commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lammps/lammps.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11xagacgxgldkx34qdzyjrjvn8x3hpl0kgzhh9zh7skpq79pwycz")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; no check target + #:make-flags + '(list "CC=mpicc" "mpi" + "LMP_INC=-DLAMMPS_GZIP \ +-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64" + "LIB=-gz -ljpeg -lpng -lavcodec") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'configure + (lambda _ + (substitute* "MAKE/Makefile.mpi" + (("SHELL =.*") + (string-append "SHELL=" (which "bash") "\n")) + (("cc ") "mpicc ")) + (substitute* "Makefile" + (("SHELL =.*") + (string-append "SHELL=" (which "bash") "\n"))))) + (add-after 'configure 'configure-modules + (lambda _ + (invoke "make" + "yes-molecule" + "yes-misc" + "yes-granular" + (string-append "HDF5_PATH=" + #$(this-package-input "hdf5"))))) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin"))) + (mkdir-p bin) + (install-file "lmp_mpi" bin))))))) + (inputs + (list ffmpeg + gfortran + gzip + hdf5 + libjpeg-turbo + libpng + openmpi + python-wrapper)) + (native-inputs (list bc)) + (home-page "https://www.lammps.org/") + (synopsis "Classical molecular dynamics simulator") + (description "LAMMPS is a classical molecular dynamics simulator +designed to run efficiently on parallel computers. LAMMPS has potentials for +solid-state materials (metals, semiconductors), soft matter (biomolecules, +polymers), and coarse-grained or mesoscopic systems. It can be used to model +atoms or, more generically, as a parallel particle simulator at the atomic, +meso, or continuum scale.") + (license license:gpl2+)))) + (define-public libbigwig (package (name "libbigwig") |