diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 146 |
1 files changed, 143 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e7b99ee61..2e4bc876d4 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 +4288,107 @@ 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 lammps-serial + (package + (inherit lammps) + (name "lammps-serial") + (arguments + (substitute-keyword-arguments (package-arguments lammps) + ((#:make-flags flags) + '(list "CC=gcc" "serial" + "LMP_INC=-DLAMMPS_GZIP \ +-DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_MEMALIGN=64" + "LIB=-gz -ljpeg -lpng -lavcodec")) + ((#:phases phases) + #~(modify-phases #$phases + (replace 'configure + (lambda _ + (substitute* "MAKE/Makefile.serial" + (("SHELL =.*") + (string-append "SHELL=" (which "bash") "\n")) + (("cc ") "gcc ")) + (substitute* "Makefile" + (("SHELL =.*") + (string-append "SHELL=" (which "bash") "\n"))))) + (replace 'install + (lambda _ + (let ((bin (string-append #$output "/bin"))) + (mkdir-p bin) + (install-file "lmp_serial" bin)))))))) + (inputs + (modify-inputs (package-inputs lammps) + (delete "openmpi"))))) + (define-public libbigwig (package (name "libbigwig") @@ -17894,12 +17996,40 @@ The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.") (license license:bsd-3))) +(define-public r-databaselinke-r + (let ((commit "cf3d6cc3d36f2e1c9a557390232e9a8ed5abb7fd") + (revision "1")) + (package + (name "r-databaselinke-r") + (version (git-version "1.7.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/DatabaseLinke.R") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hk76sb3w1v8a7c1knpc572ypsbgqlrv0p49c9y55a0dr12n16s1")))) + (properties `((upstream-name . "DatabaseLinke.R"))) + (build-system r-build-system) + (propagated-inputs (list r-readwriter)) + (home-page "https://github.com/vertesy/DatabaseLinke.R") + (synopsis + "Parse links to databases from your list of gene symbols") + (description + "This package provides a set of functions to parse and open (search +query) links to genomics related and other websites for R. Useful when you +want to explore e.g.: the function of a set of differentially expressed +genes.") + (license license:gpl3)))) + (define-public r-seurat-utils - (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5") + (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d") (revision "1")) (package (name "r-seurat-utils") - (version (git-version "1.6.5" revision commit)) + (version (git-version "2.5.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -17908,12 +18038,15 @@ facilitates comparative analysis of known RNA families.") (file-name (git-file-name name version)) (sha256 (base32 - "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762")))) + "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd")))) (properties `((upstream-name . "Seurat.utils"))) (build-system r-build-system) (propagated-inputs (list r-codeandroll2 r-cowplot + r-databaselinke-r r-dplyr + r-enhancedvolcano + r-foreach r-ggcorrplot r-ggexpress r-ggplot2 @@ -17921,15 +18054,21 @@ facilitates comparative analysis of known RNA families.") r-ggrepel r-hgnchelper r-htmlwidgets + r-job + r-magrittr r-markdownhelpers r-markdownreports r-matrix r-matrixstats + r-pheatmap + r-plotly r-princurve + r-qs r-r-utils r-readr r-readwriter r-reshape2 + r-rstudioapi r-scales r-seurat r-soupx @@ -17938,6 +18077,7 @@ facilitates comparative analysis of known RNA families.") r-stringr r-tibble r-tictoc + r-tidyverse r-vroom)) (home-page "https://github.com/vertesy/Seurat.utils") (synopsis "Collection of utility functions for Seurat") |