diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 135 |
1 files changed, 29 insertions, 106 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e3c24aeb57..0a30d0921f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11783,80 +11783,19 @@ The following file formats are supported: @end enumerate\n") (license license:bsd-3))) -(define spdlog-for-salmon - (package - (name "spdlog") - (version "0.14.0") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/COMBINE-lab/spdlog.git") - (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q")))) - (build-system cmake-build-system) - (home-page "https://github.com/COMBINE-lab/spdlog") - (synopsis "Very fast C++ logging library") - (description "Spdlog is a very fast header-only C++ logging library with -performance as its primary goal.") - (license license:expat))) - -;; This is a modified variant of bwa for use with Salmon. It installs a -;; library to avoid having to build this as part of Salmon. -(define bwa-for-salmon - (package (inherit bwa) - (name "bwa") - (version "0.7.12.5") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/COMBINE-lab/bwa.git") - (commit (string-append "v" version)))) - (file-name (string-append "bwa-for-salmon-" version "-checkout")) - (sha256 - (base32 - "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb")))) - (build-system gnu-build-system) - (arguments - '(#:tests? #f ;no "check" target - #:phases - (modify-phases %standard-phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (lib (string-append out "/lib")) - (doc (string-append out "/share/doc/bwa")) - (man (string-append out "/share/man/man1")) - (inc (string-append out "/include/bwa"))) - (install-file "bwa" bin) - (install-file "README.md" doc) - (install-file "bwa.1" man) - (install-file "libbwa.a" lib) - (mkdir-p lib) - (mkdir-p inc) - (for-each (lambda (file) - (install-file file inc)) - (find-files "." "\\.h$"))) - #t)) - ;; no "configure" script - (delete 'configure)))))) - (define-public salmon (package (name "salmon") - (version "0.9.1") + (version "0.13.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/COMBINE-lab/salmon.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a")) + "1i2z4aivicmiixdz9bxalp7vmfzi3k92fxa63iqa8kgvfw5a4aq5")) (modules '((guix build utils))) (snippet '(begin @@ -11890,7 +11829,7 @@ performance as its primary goal.") (add-after 'unpack 'do-not-look-for-boost (lambda* (#:key inputs #:allow-other-keys) (substitute* "CMakeLists.txt" - (("find_package\\(Boost 1\\.53\\.0") "#")) + (("find_package\\(Boost 1\\.59\\.0") "#")) #t)) (add-after 'unpack 'do-not-phone-home (lambda _ @@ -11904,66 +11843,51 @@ performance as its primary goal.") (rapmap (assoc-ref inputs "rapmap"))) (mkdir-p src) (mkdir-p include) - (for-each (lambda (file) - (install-file file src)) - (find-files (string-append rapmap "/src") "\\.(c|cpp)")) + (copy-recursively (string-append rapmap "/src") src) (copy-recursively (string-append rapmap "/include") include) (for-each delete-file '("external/install/include/rapmap/xxhash.h" "external/install/include/rapmap/FastxParser.hpp" "external/install/include/rapmap/concurrentqueue.h" "external/install/include/rapmap/FastxParserThreadUtils.hpp" "external/install/src/rapmap/FastxParser.cpp" - "external/install/src/rapmap/xxhash.c"))) + "external/install/src/rapmap/xxhash.c")) + (delete-file-recursively "external/install/include/rapmap/spdlog")) #t)) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + ;; Don't prefer static libs + (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") + (("set\\(TBB_LIBRARIES") "message(") + ;; Don't download anything + (("DOWNLOAD_COMMAND") "DOWNLOAD_COMMAND echo") + (("externalproject_add\\(libcereal") "message(") + (("externalproject_add\\(libgff") "message(") + (("externalproject_add\\(libtbb") "message(") + (("externalproject_add\\(libdivsufsort") "message(") + (("externalproject_add\\(libstadenio") "message(") + (("externalproject_add_step\\(") "message(")) (substitute* "src/CMakeLists.txt" - (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..") - (string-append (assoc-ref inputs "jellyfish") - "/include/jellyfish-" ,(package-version jellyfish))) - (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a") - (string-append (assoc-ref inputs "jellyfish") - "/lib/libjellyfish-2.0.a")) + (("add_dependencies") "#") + (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a") + (string-append (assoc-ref inputs "libstadenio-for-salmon") + "/lib/libstaden-read.so")) (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a") (string-append (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort.so")) - (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a") - (string-append (assoc-ref inputs "libstadenio-for-salmon") - "/lib/libstaden-read.a")) - (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a") - (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a")) (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a") (string-append (assoc-ref inputs "libdivsufsort") - "/lib/libdivsufsort64.so"))) - (substitute* "CMakeLists.txt" - ;; Don't prefer static libs - (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") - (("set\\(TBB_LIBRARIES") "message(") - (("find_package\\(Jellyfish.*") "") - (("ExternalProject_Add\\(libcereal") "message(") - (("ExternalProject_Add\\(libbwa") "message(") - (("ExternalProject_Add\\(libjellyfish") "message(") - (("ExternalProject_Add\\(libgff") "message(") - (("ExternalProject_Add\\(libtbb") "message(") - (("ExternalProject_Add\\(libspdlog") "message(") - (("ExternalProject_Add\\(libdivsufsort") "message(") - (("ExternalProject_Add\\(libstadenio") "message(") - (("ExternalProject_Add_Step\\(") "message(")) + "/lib/libdivsufsort64.so")) + (("lib/libdivsufsort.a") "/lib/libdivsufsort.so")) ;; Ensure that all headers can be found (setenv "CPLUS_INCLUDE_PATH" (string-append (getenv "CPLUS_INCLUDE_PATH") ":" - (assoc-ref inputs "bwa") - "/include/bwa" - ":" (assoc-ref inputs "eigen") "/include/eigen3")) (setenv "CPATH" - (string-append (assoc-ref inputs "bwa") - "/include/bwa" - ":" - (assoc-ref inputs "eigen") + (string-append (assoc-ref inputs "eigen") "/include/eigen3")) #t)) ;; CMAKE_INSTALL_PREFIX does not exist when the tests are @@ -11976,7 +11900,6 @@ performance as its primary goal.") #t))))) (inputs `(("boost" ,boost) - ("bwa" ,bwa-for-salmon) ("bzip2" ,bzip2) ("cereal" ,cereal) ("eigen" ,eigen) @@ -11988,16 +11911,16 @@ performance as its primary goal.") (file-name (string-append "rapmap-salmon-v" version "-checkout")) (sha256 (base32 - "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p")))) + "1biplxf0csc7a8h1wf219b0vmjkvw6wk2zylhdklb577kgmihdms")))) ("jemalloc" ,jemalloc) - ("jellyfish" ,jellyfish) ("libgff" ,libgff) ("tbb" ,tbb) ("libdivsufsort" ,libdivsufsort) ("libstadenio-for-salmon" ,libstadenio-for-salmon) - ("spdlog-for-salmon" ,spdlog-for-salmon) ("xz" ,xz) ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/COMBINE-lab/salmon") (synopsis "Quantification from RNA-seq reads using lightweight alignments") (description "Salmon is a program to produce highly-accurate, |