diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 179 |
1 files changed, 116 insertions, 63 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8ecea013c..d18d5d8611 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9308,6 +9308,69 @@ viewer.") (delete 'patch-tests) (delete 'configure)))))))) +(define-public morpheus + (package + (name "morpheus") + (version "2.3.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/morpheus.lab/morpheus") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jyzbkz8d39kjicrk3ihcx7yvq5wsynvnlcw922bqqsw8nwnn12c")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "3rdparty/eigen") + (substitute* '("morpheus/core/cpm_shape_tracker.cpp" + "morpheus/core/membranemapper.h" + "morpheus/testing/components/motility/directed_motion_test.cpp" + "morpheus/testing/components/interaction/generator_cell_sorting.cpp" + "morpheus/testing/components/interaction/test_cell_sorting.cpp" + "morpheus/testing/core/cpm/generator_csm_plane.cpp" + "morpheus/testing/test_operators.h") + (("#include \"eigen/") "#include \"eigen3/")))))) + ;; This is for a different Morpheus. + (properties '((lint-hidden-cve "CVE-2022-31261"))) + (build-system cmake-build-system) + (arguments + (list + #:configure-flags + '(list "-DMORPHEUS_GUI=OFF" + "-DBUILD_TESTING=ON" + "-DDOWNLOAD_XTENSOR=OFF") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-gtest-download + (lambda _ + (substitute* "3rdparty/CMakeLists.txt" + (("add_subdirectory\\(GTest\\)") "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "--output-junit" "test_results.xml"))))))) + (inputs (list boost + eigen + file + gnuplot + libtiff + libxslt + xsimd + xtensor + xtl + zlib)) + (native-inputs + (list doxygen googletest xxd)) + (home-page "https://gitlab.com/morpheus.lab/morpheus") + (synopsis "Multicellular simulation") + (description + "Morpheus is a modeling and simulation environment for the study of +multi-scale and multicellular systems.") + (license license:bsd-3))) + (define-public mosaik (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) (package @@ -11612,30 +11675,6 @@ clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.") (license license:gpl3))) -(define-public r-tictoc - (package - (name "r-tictoc") - (version "1.2") - (source (origin - (method url-fetch) - (uri (cran-uri "tictoc" version)) - (sha256 - (base32 - "037jbwb58mj5asf3kr6hpf3fy9c6fkinnd8hbpfb141a2jsa8pph")))) - (properties `((upstream-name . "tictoc"))) - (build-system r-build-system) - (home-page "https://github.com/jabiru/tictoc") - (synopsis - "Time R scripts and implementations of stack and list structures") - (description - "The tictoc package provides the timing functions @code{tic} and -@code{toc} that can be nested. It provides an alternative to -@code{system.time()} with a different syntax similar to that in another -well-known software package. @code{tic} and @code{toc} are easy to use, and -are especially useful when timing several sections in more than a few lines of -code.") - (license license:asl2.0))) - (define-public r-tsis (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc") (revision "1")) @@ -12351,6 +12390,59 @@ Needleman-Wunsch).") ;; Dual licensed; also includes public domain source. (license (list license:gpl3 license:bsd-2)))) +(define-public pairadise + (package + (name "pairadise") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Xinglab/PAIRADISE") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ycwcqabm4zdng0a7j593g35d5yzvvwm7dyi3b8s19zdi4rjzrwd")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "pairadise"))) + (add-before 'build '2to3 + (lambda _ (invoke "2to3" "--write" "--nobackups" ".")))))) + (inputs (list star)) + (propagated-inputs (list python-pysam)) + (home-page "https://github.com/Xinglab/PAIRADISE") + (synopsis "Paired replicate analysis of allelic differential splicing events") + (description + "PAIRADISE is a method for detecting @dfn{allele-specific alternative +splicing} (ASAS) from RNA-seq data. Unlike conventional approaches that +detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals +across multiple individuals in a population. By treating the two alleles of +an individual as paired, and multiple individuals sharing a heterozygous SNP +as replicates, PAIRADISE formulates ASAS detection as a statistical problem +for identifying differential alternative splicing from RNA-seq data with +paired replicates.") + (license license:gpl3+))) + +(define-public r-pairadise + (package + (inherit pairadise) + (name "r-pairadise") + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "pairadise/src/pairadise_model")))))) + (inputs '()) + (propagated-inputs (list r-doparallel r-foreach r-iterators r-nloptr)) + (license license:expat))) + (define-public pardre (package (name "pardre") @@ -16417,45 +16509,6 @@ sequencing data in microbiome studies with the Dirichlet-tree Multinomial Mixtures.") (license license:cc0)))) -(define-public r-dyngen - (package - (name "r-dyngen") - (version "1.0.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "dyngen" version)) - (sha256 - (base32 - "095jqn1rd83qm3ayca9hmv6bhlaa2c338020l46vniq8n38kbnra")))) - (properties `((upstream-name . "dyngen"))) - (build-system r-build-system) - (propagated-inputs - (list r-assertthat - r-dplyr - r-dynutils - r-ggplot2 - r-ggraph - r-ggrepel - r-gillespiessa2 - r-igraph - r-lmds - r-matrix - r-patchwork - r-pbapply - r-purrr - r-rlang - r-tibble - r-tidygraph - r-tidyr - r-viridis)) - (home-page "https://github.com/dynverse/dyngen") - (synopsis "Multi-Modal simulator for single-cell omics analyses") - (description - "This package provides a multi-modal simulation engine for studying -dynamic cellular processes at single-cell resolution.") - (license license:expat))) - ;; Needed for r-liana (define-public r-omnipathr/devel (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a") |