diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 198 |
1 files changed, 100 insertions, 98 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5b47eedf5..249b956c88 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10296,7 +10296,7 @@ The following file formats are supported: (define-public salmon (package (name "salmon") - (version "1.6.0") + (version "1.9.0") (source (origin (method git-fetch) (uri (git-reference @@ -10305,104 +10305,112 @@ The following file formats are supported: (file-name (git-file-name name version)) (sha256 (base32 - "1wb5wl0rc77svbwq6zvak5h7pf9acw3di0vz5i3gqyhg5l6qd736")) + "1370ry3jpj05gplzyny44mqg77a29a6gp8ijmjz135d2igf956r8")) (modules '((guix build utils))) (snippet ;; Delete bundled headers for eigen3. '(delete-file-recursively "include/eigen3/")))) (build-system cmake-build-system) (arguments - `(#:configure-flags - ,#~(list (string-append "-Dlibgff_DIR=" - #$(this-package-input "libgff") "/lib") - "-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\"" - "-Dlibgff_FOUND=TRUE" - "-DTBB_FOUND=TRUE" - #$(string-append "-DTBB_VERSION=" (package-version tbb-2020)) - "-DTBB_LIBRARIES=tbb -ltbbmalloc" - "-DFETCHED_PUFFERFISH=TRUE" - "-DUSE_SHARED_LIBS=TRUE") + (list + #:configure-flags + #~(list (string-append "-Dlibgff_DIR=" + #$(this-package-input "libgff") "/lib") + "-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\"" + "-Dlibgff_FOUND=TRUE" + "-DTBB_FOUND=TRUE" + #$(string-append "-DTBB_VERSION=" (package-version tbb)) + "-DFETCHED_PUFFERFISH=TRUE" + "-DUSE_SHARED_LIBS=TRUE") #:phases - (modify-phases %standard-phases - (add-after 'unpack 'prepare-pufferfish - (lambda* (#:key inputs #:allow-other-keys) - (copy-recursively (assoc-ref inputs "pufferfish") - "external/pufferfish") - ;; This test isn't working correctly, so compilation aborts. - (substitute* "external/pufferfish/include/string_view.hpp" - (("#if __has_include\\(<string_view>\\)") - "#if 0")) - (let ((headers "external/install/pufferfish/include/pufferfish") - (source "external/install/src/pufferfish")) - (mkdir-p headers) - (mkdir-p source) - (for-each (lambda (file) - (install-file (string-append "external/pufferfish/include/" file) - headers)) - (list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp" - "Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp" - "CanonicalKmerIterator.hpp" - "PufferfishBaseIndex.hpp" - "PufferfishIndex.hpp" - "PufferfishSparseIndex.hpp" - "PufferfishLossyIndex.hpp" - "PufferfishTypes.hpp" - "rank9b.hpp" "rank9sel.hpp" "macros.hpp" - "select.hpp" "Util.hpp" - "PairedAlignmentFormatter.hpp" - "SelectiveAlignmentUtils.hpp" - "PuffAligner.hpp" "MemCollector.hpp" - "MemChainer.hpp" "CommonTypes.hpp" - "SAMWriter.hpp" "PufferfishConfig.hpp" - "BulkChunk.hpp" "BinWriter.hpp")) - (for-each (lambda (dir) - (copy-recursively - (string-append "external/pufferfish/include/" dir) - (string-append headers "/" dir))) - (list "libdivide" - "ksw2pp" - "compact_vector" - "metro" - "chobo" - "sparsepp" - "simde" - "tsl")) - (copy-recursively - (string-append "external/pufferfish/src/metro/") - (string-append source "/metro")) - (install-file - (string-append "external/pufferfish/src/rank9b.cpp") - source) - - ;; Do not complain about not having built libtbb - (substitute* "external/pufferfish/external/twopaco/CMakeLists.txt" - (("add_dependencies.*") ""))))) - (add-after 'unpack 'do-not-phone-home - (lambda _ - (substitute* "src/Salmon.cpp" - (("getVersionMessage\\(\\)") "\"\"")))) - (add-after 'unpack 'use-system-libraries - (lambda* (#:key inputs #:allow-other-keys) - ;; Ensure that all headers can be found - (setenv "CPLUS_INCLUDE_PATH" - (string-append (or (getenv "CPLUS_INCLUDE_PATH") "") - ":" - (getcwd) "/external/install/pufferfish/include:" - (assoc-ref inputs "eigen") - "/include/eigen3")))) - (add-after 'unpack 'fix-error-message-in-tests - (lambda _ - (substitute* "cmake/TestSalmonQuasi.cmake" - (("SALMON_QUASI_INDEX_COMMAND") - "SALMON_QUASI_INDEX_CMD"))))))) + '(modify-phases %standard-phases + (add-after 'unpack 'prepare-pufferfish + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "pufferfish") + "external/pufferfish") + ;; This test isn't working correctly, so compilation aborts. + (substitute* "external/pufferfish/include/string_view.hpp" + (("#if __has_include\\(<string_view>\\)") + "#if 0")) + (let ((headers "external/install/pufferfish/include/pufferfish") + (source "external/install/src/pufferfish")) + (mkdir-p headers) + (mkdir-p source) + (for-each (lambda (file) + (install-file (string-append "external/pufferfish/include/" file) + headers)) + (list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp" + "Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp" + "CanonicalKmerIterator.hpp" + "PufferfishBaseIndex.hpp" + "PufferfishIndex.hpp" + "PufferfishSparseIndex.hpp" + "PufferfishLossyIndex.hpp" + "PufferfishTypes.hpp" + "rank9b.hpp" "rank9sel.hpp" "macros.hpp" + "select.hpp" "Util.hpp" + "PairedAlignmentFormatter.hpp" + "SelectiveAlignmentUtils.hpp" + "PuffAligner.hpp" "MemCollector.hpp" + "MemChainer.hpp" "CommonTypes.hpp" + "SAMWriter.hpp" "PufferfishConfig.hpp" + "BulkChunk.hpp" "BinWriter.hpp")) + + (for-each (lambda (dir) + (copy-recursively + (string-append "external/pufferfish/include/" dir) + (string-append headers "/" dir))) + (list "libdivide" + "ksw2pp" + "compact_vector" + "itlib" + "metro" + "chobo" + "sparsepp" + "simde" + "tsl")) + (copy-recursively + (string-append "external/pufferfish/src/metro/") + (string-append source "/metro")) + (install-file + (string-append "external/pufferfish/src/rank9b.cpp") + source) + + ;; Do not complain about not having built libtbb + (substitute* "external/pufferfish/external/twopaco/CMakeLists.txt" + (("add_dependencies.*") ""))))) + (add-after 'unpack 'do-not-phone-home + (lambda _ + (substitute* "src/Salmon.cpp" + (("getVersionMessage\\(\\)") "\"\"")))) + (add-after 'unpack 'use-system-libraries + (lambda* (#:key inputs #:allow-other-keys) + ;; Ensure that all headers can be found + (setenv "CPLUS_INCLUDE_PATH" + (string-append (or (getenv "CPLUS_INCLUDE_PATH") "") + ":" + (getcwd) "/external/install/pufferfish/include:" + (assoc-ref inputs "eigen") + "/include/eigen3")))) + (add-after 'unpack 'fix-error-message-in-tests + (lambda _ + (substitute* "cmake/TestSalmonQuasi.cmake" + (("SALMON_QUASI_INDEX_COMMAND") + "SALMON_QUASI_INDEX_CMD"))))))) (inputs - `(("boost" ,boost) - ("bzip2" ,bzip2) - ("cereal" ,cereal-1.3.0) - ("curl" ,curl) - ("eigen" ,eigen) - ("jemalloc" ,jemalloc) - ("libgff" ,libgff) + (list boost + bzip2 + cereal-1.3.0 + curl + eigen + jemalloc + libgff + tbb + libstadenio-for-salmon + xz + zlib)) + (native-inputs + `(("pkg-config" ,pkg-config) ("pufferfish" ,(origin (method git-fetch) (uri (git-reference @@ -10411,13 +10419,7 @@ The following file formats are supported: (file-name (git-file-name "pufferfish" version)) (sha256 (base32 - "0jakgpbanl6cs23x3g26iab54p7zylcf9v8vc32ps57smp8wql52")))) - ("tbb" ,tbb-2020) - ("libstadenio-for-salmon" ,libstadenio-for-salmon) - ("xz" ,xz) - ("zlib" ,zlib))) - (native-inputs - (list pkg-config)) + "048a006mc2d0h78ym58mv67hl1pj480ilc5ifq0rlzfdyyfs1b8i")))))) (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, |