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authorRicardo Wurmus <rekado@elephly.net>2024-03-14 21:01:00 +0100
committerRicardo Wurmus <rekado@elephly.net>2024-03-14 21:01:37 +0100
commitefe62c5ed38a09d7467a6c1c3d5f509d284ad290 (patch)
tree991d192f4b25148607294ca69432f15e916b40d6 /gnu/packages
parent7319b4d5286d31a9c6a889e81af72308efdaab41 (diff)
gnu: Add morpheus.
* gnu/packages/bioinformatics.scm (morpheus): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de> Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm63
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b8ecea013c..dd51f73d5b 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