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gnu: express: Adjust bamtools location. 

* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
 #T.
master
Ricardo Wurmus 2023-04-27 09:25:26 +02:00
parent f196b3b7a5
commit 9d82c475a3
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GPG Key ID: 197A5888235FACAC
1 changed files with 21 additions and 21 deletions
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gnu/packages/bioinformatics.scm
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@ -4584,27 +4584,27 @@ dynamic programming or a variety of heuristics.")
"18nb22n7x820fzjngf4qgyb3mspqkw7xyk7v7s5ps6wfrd8qwscb")))) "18nb22n7x820fzjngf4qgyb3mspqkw7xyk7v7s5ps6wfrd8qwscb"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments (arguments
`(#:tests? #f ;no "check" target (list
#:phases #:tests? #f ;no "check" target
(modify-phases %standard-phases #:phases
(add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths #~(modify-phases %standard-phases
(lambda* (#:key inputs #:allow-other-keys) (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
(substitute* "CMakeLists.txt" (lambda* (#:key inputs #:allow-other-keys)
(("set\\(Boost_USE_STATIC_LIBS ON\\)") (substitute* "CMakeLists.txt"
"set(Boost_USE_STATIC_LIBS OFF)") (("set\\(Boost_USE_STATIC_LIBS ON\\)")
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") "set(Boost_USE_STATIC_LIBS OFF)")
(string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
(substitute* "src/CMakeLists.txt" (search-input-directory inputs "/include/bamtools"))
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") (("\\$\\{PROJECT_SOURCE_DIR\\}/bamtools/lib/libbamtools.a")
(string-append (assoc-ref inputs "bamtools") "/lib")) (search-input-file inputs "/lib/libbamtools.so"))
(("libprotobuf.a") "libprotobuf.so")) (("libbamtools.a") "libbamtools.so"))
#t)) (substitute* "src/CMakeLists.txt"
(add-after 'unpack 'remove-update-check (("libprotobuf.a") "libprotobuf.so"))))
(lambda _ (add-after 'unpack 'remove-update-check
(substitute* "src/main.cpp" (lambda _
(("#include \"update_check.h\"") "") (substitute* "src/main.cpp"
(("check_version\\(PACKAGE_VERSION\\);") "")) (("#include \"update_check.h\"") "")
#t))))) (("check_version\\(PACKAGE_VERSION\\);") "")))))))
(inputs (inputs
(list boost bamtools protobuf zlib)) (list boost bamtools protobuf zlib))
(home-page "http://bio.math.berkeley.edu/eXpress") (home-page "http://bio.math.berkeley.edu/eXpress")