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gnu: salmon: Update to 0.13.1. 

* gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1.
[arguments]: Adjust "do-not-look-for-boost" build phase; adjust
"prepare-rapmap" phase; adjust "use-system-libraries" phase.
[inputs]: Remove bwa, jellyfish, spdlog-for-salmon.
[native-inputs]: Add pkg-config.
(spdlog-for-salmon, bwa-for-salmon): Remove variables.
This commit is contained in:
Ricardo Wurmus 2019-05-23 16:32:21 +02:00
parent f918a296e8
commit a9150d4c23
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1 changed files with 31 additions and 108 deletions
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@ -11783,80 +11783,19 @@ The following file formats are supported:
@end enumerate\n") @end enumerate\n")
(license license:bsd-3))) (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 (define-public salmon
(package (package
(name "salmon") (name "salmon")
(version "0.9.1") (version "0.13.1")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/COMBINE-lab/salmon.git") (url "https://github.com/COMBINE-lab/salmon.git")
(commit (string-append "v" version)))) (commit (string-append "v" version))))
(file-name (string-append name "-" version "-checkout")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a")) "1i2z4aivicmiixdz9bxalp7vmfzi3k92fxa63iqa8kgvfw5a4aq5"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
@ -11890,7 +11829,7 @@ performance as its primary goal.")
(add-after 'unpack 'do-not-look-for-boost (add-after 'unpack 'do-not-look-for-boost
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt" (substitute* "CMakeLists.txt"
(("find_package\\(Boost 1\\.53\\.0") "#")) (("find_package\\(Boost 1\\.59\\.0") "#"))
#t)) #t))
(add-after 'unpack 'do-not-phone-home (add-after 'unpack 'do-not-phone-home
(lambda _ (lambda _
@ -11904,66 +11843,51 @@ performance as its primary goal.")
(rapmap (assoc-ref inputs "rapmap"))) (rapmap (assoc-ref inputs "rapmap")))
(mkdir-p src) (mkdir-p src)
(mkdir-p include) (mkdir-p include)
(for-each (lambda (file) (copy-recursively (string-append rapmap "/src") src)
(install-file file src))
(find-files (string-append rapmap "/src") "\\.(c|cpp)"))
(copy-recursively (string-append rapmap "/include") include) (copy-recursively (string-append rapmap "/include") include)
(for-each delete-file '("external/install/include/rapmap/xxhash.h" (for-each delete-file '("external/install/include/rapmap/xxhash.h"
"external/install/include/rapmap/FastxParser.hpp" "external/install/include/rapmap/FastxParser.hpp"
"external/install/include/rapmap/concurrentqueue.h" "external/install/include/rapmap/concurrentqueue.h"
"external/install/include/rapmap/FastxParserThreadUtils.hpp" "external/install/include/rapmap/FastxParserThreadUtils.hpp"
"external/install/src/rapmap/FastxParser.cpp" "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)) #t))
(add-after 'unpack 'use-system-libraries (add-after 'unpack 'use-system-libraries
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(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"))
(("\\$\\{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" (substitute* "CMakeLists.txt"
;; Don't prefer static libs ;; Don't prefer static libs
(("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
(("set\\(TBB_LIBRARIES") "message(") (("set\\(TBB_LIBRARIES") "message(")
(("find_package\\(Jellyfish.*") "") ;; Don't download anything
(("ExternalProject_Add\\(libcereal") "message(") (("DOWNLOAD_COMMAND") "DOWNLOAD_COMMAND echo")
(("ExternalProject_Add\\(libbwa") "message(") (("externalproject_add\\(libcereal") "message(")
(("ExternalProject_Add\\(libjellyfish") "message(") (("externalproject_add\\(libgff") "message(")
(("ExternalProject_Add\\(libgff") "message(") (("externalproject_add\\(libtbb") "message(")
(("ExternalProject_Add\\(libtbb") "message(") (("externalproject_add\\(libdivsufsort") "message(")
(("ExternalProject_Add\\(libspdlog") "message(") (("externalproject_add\\(libstadenio") "message(")
(("ExternalProject_Add\\(libdivsufsort") "message(") (("externalproject_add_step\\(") "message("))
(("ExternalProject_Add\\(libstadenio") "message(") (substitute* "src/CMakeLists.txt"
(("ExternalProject_Add_Step\\(") "message(")) (("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/libdivsufsort64.a")
(string-append (assoc-ref inputs "libdivsufsort")
"/lib/libdivsufsort64.so"))
(("lib/libdivsufsort.a") "/lib/libdivsufsort.so"))
;; Ensure that all headers can be found ;; Ensure that all headers can be found
(setenv "CPLUS_INCLUDE_PATH" (setenv "CPLUS_INCLUDE_PATH"
(string-append (getenv "CPLUS_INCLUDE_PATH") (string-append (getenv "CPLUS_INCLUDE_PATH")
":"
(assoc-ref inputs "bwa")
"/include/bwa"
":" ":"
(assoc-ref inputs "eigen") (assoc-ref inputs "eigen")
"/include/eigen3")) "/include/eigen3"))
(setenv "CPATH" (setenv "CPATH"
(string-append (assoc-ref inputs "bwa") (string-append (assoc-ref inputs "eigen")
"/include/bwa"
":"
(assoc-ref inputs "eigen")
"/include/eigen3")) "/include/eigen3"))
#t)) #t))
;; CMAKE_INSTALL_PREFIX does not exist when the tests are ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
@ -11976,7 +11900,6 @@ performance as its primary goal.")
#t))))) #t)))))
(inputs (inputs
`(("boost" ,boost) `(("boost" ,boost)
("bwa" ,bwa-for-salmon)
("bzip2" ,bzip2) ("bzip2" ,bzip2)
("cereal" ,cereal) ("cereal" ,cereal)
("eigen" ,eigen) ("eigen" ,eigen)
@ -11988,16 +11911,16 @@ performance as its primary goal.")
(file-name (string-append "rapmap-salmon-v" version "-checkout")) (file-name (string-append "rapmap-salmon-v" version "-checkout"))
(sha256 (sha256
(base32 (base32
"1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p")))) "1biplxf0csc7a8h1wf219b0vmjkvw6wk2zylhdklb577kgmihdms"))))
("jemalloc" ,jemalloc) ("jemalloc" ,jemalloc)
("jellyfish" ,jellyfish)
("libgff" ,libgff) ("libgff" ,libgff)
("tbb" ,tbb) ("tbb" ,tbb)
("libdivsufsort" ,libdivsufsort) ("libdivsufsort" ,libdivsufsort)
("libstadenio-for-salmon" ,libstadenio-for-salmon) ("libstadenio-for-salmon" ,libstadenio-for-salmon)
("spdlog-for-salmon" ,spdlog-for-salmon)
("xz" ,xz) ("xz" ,xz)
("zlib" ,zlib))) ("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://github.com/COMBINE-lab/salmon") (home-page "https://github.com/COMBINE-lab/salmon")
(synopsis "Quantification from RNA-seq reads using lightweight alignments") (synopsis "Quantification from RNA-seq reads using lightweight alignments")
(description "Salmon is a program to produce highly-accurate, (description "Salmon is a program to produce highly-accurate,