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.master
Ricardo Wurmus
parent
f918a296e8
commit
a9150d4c23
|
|
@ -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* "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"
|
||||
;; 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("))
|
||||
;; 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"
|
||||
(("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
|
||||
(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,
|
||||
|
|
|
|||
Loading…
Reference in New Issue