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gnu: salmon: Update to 1.9.0. 

* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0.
[arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish
itlib headers.
[inputs]: Use new label-less list; move pufferfish origin from here...
[native-inputs]: ...to here.
master
Ricardo Wurmus 2022-09-30 22:43:21 +02:00
parent 729ce5fcf8
commit 1266b9ed11
No known key found for this signature in database
GPG Key ID: 197A5888235FACAC
1 changed files with 99 additions and 97 deletions
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gnu/packages/bioinformatics.scm
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@ -10296,7 +10296,7 @@ The following file formats are supported:
(define-public salmon (define-public salmon
(package (package
(name "salmon") (name "salmon")
(version "1.6.0") (version "1.9.0")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -10305,25 +10305,25 @@ The following file formats are supported:
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1wb5wl0rc77svbwq6zvak5h7pf9acw3di0vz5i3gqyhg5l6qd736")) "1370ry3jpj05gplzyny44mqg77a29a6gp8ijmjz135d2igf956r8"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
;; Delete bundled headers for eigen3. ;; Delete bundled headers for eigen3.
'(delete-file-recursively "include/eigen3/")))) '(delete-file-recursively "include/eigen3/"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments (arguments
`(#:configure-flags (list
,#~(list (string-append "-Dlibgff_DIR=" #:configure-flags
#~(list (string-append "-Dlibgff_DIR="
#$(this-package-input "libgff") "/lib") #$(this-package-input "libgff") "/lib")
"-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\"" "-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\""
"-Dlibgff_FOUND=TRUE" "-Dlibgff_FOUND=TRUE"
"-DTBB_FOUND=TRUE" "-DTBB_FOUND=TRUE"
#$(string-append "-DTBB_VERSION=" (package-version tbb-2020)) #$(string-append "-DTBB_VERSION=" (package-version tbb))
"-DTBB_LIBRARIES=tbb -ltbbmalloc"
"-DFETCHED_PUFFERFISH=TRUE" "-DFETCHED_PUFFERFISH=TRUE"
"-DUSE_SHARED_LIBS=TRUE") "-DUSE_SHARED_LIBS=TRUE")
#:phases #:phases
(modify-phases %standard-phases '(modify-phases %standard-phases
(add-after 'unpack 'prepare-pufferfish (add-after 'unpack 'prepare-pufferfish
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(copy-recursively (assoc-ref inputs "pufferfish") (copy-recursively (assoc-ref inputs "pufferfish")
@ -10355,6 +10355,7 @@ The following file formats are supported:
"MemChainer.hpp" "CommonTypes.hpp" "MemChainer.hpp" "CommonTypes.hpp"
"SAMWriter.hpp" "PufferfishConfig.hpp" "SAMWriter.hpp" "PufferfishConfig.hpp"
"BulkChunk.hpp" "BinWriter.hpp")) "BulkChunk.hpp" "BinWriter.hpp"))
(for-each (lambda (dir) (for-each (lambda (dir)
(copy-recursively (copy-recursively
(string-append "external/pufferfish/include/" dir) (string-append "external/pufferfish/include/" dir)
@ -10362,6 +10363,7 @@ The following file formats are supported:
(list "libdivide" (list "libdivide"
"ksw2pp" "ksw2pp"
"compact_vector" "compact_vector"
"itlib"
"metro" "metro"
"chobo" "chobo"
"sparsepp" "sparsepp"
@ -10396,13 +10398,19 @@ The following file formats are supported:
(("SALMON_QUASI_INDEX_COMMAND") (("SALMON_QUASI_INDEX_COMMAND")
"SALMON_QUASI_INDEX_CMD"))))))) "SALMON_QUASI_INDEX_CMD")))))))
(inputs (inputs
`(("boost" ,boost) (list boost
("bzip2" ,bzip2) bzip2
("cereal" ,cereal-1.3.0) cereal-1.3.0
("curl" ,curl) curl
("eigen" ,eigen) eigen
("jemalloc" ,jemalloc) jemalloc
("libgff" ,libgff) libgff
tbb
libstadenio-for-salmon
xz
zlib))
(native-inputs
`(("pkg-config" ,pkg-config)
("pufferfish" ,(origin ("pufferfish" ,(origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -10411,13 +10419,7 @@ The following file formats are supported:
(file-name (git-file-name "pufferfish" version)) (file-name (git-file-name "pufferfish" version))
(sha256 (sha256
(base32 (base32
"0jakgpbanl6cs23x3g26iab54p7zylcf9v8vc32ps57smp8wql52")))) "048a006mc2d0h78ym58mv67hl1pj480ilc5ifq0rlzfdyyfs1b8i"))))))
("tbb" ,tbb-2020)
("libstadenio-for-salmon" ,libstadenio-for-salmon)
("xz" ,xz)
("zlib" ,zlib)))
(native-inputs
(list 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,