diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 105 |
1 files changed, 45 insertions, 60 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 62d0dc93e1..4f8c266a3b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7271,8 +7271,6 @@ bases are detected.") (bin (string-append #$output "/bin/"))) (mkdir-p bin) (copy-recursively "." share) - (delete-file (string-append share "/Chrysalis/build/CMakeFiles/CMakeOutput.log")) - (delete-file (string-append share "/Inchworm/build/CMakeFiles/CMakeOutput.log")) (wrap-program (string-append share "Trinity") `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) @@ -7326,7 +7324,7 @@ bases are detected.") (list coreutils gzip which)) - (native-inputs (list cmake)) + (native-inputs (list cmake-minimal)) (home-page "https://github.com/trinityrnaseq/trinityrnaseq/wiki") (synopsis "Trinity RNA-Seq de novo transcriptome assembly") (description "Trinity assembles transcript sequences from Illumina RNA-Seq @@ -8455,7 +8453,7 @@ comment or quality sections.") (define-public gemma (package (name "gemma") - (version "0.98.3") + (version "v0.98.5") (source (origin (method git-fetch) (uri (git-reference @@ -8464,7 +8462,7 @@ comment or quality sections.") (file-name (git-file-name name version)) (sha256 (base32 - "1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7")) + "1dm8pf1fbdmv2yiz5aybcvk3050m5350gq8xlr4j6swzm3wwhydn")) (modules '((guix build utils))) (snippet '(begin @@ -11370,7 +11368,6 @@ seamless support for BCF and VCF files.") (list #:configure-flags '(list "-DMORPHEUS_GUI=OFF" - "-DBUILD_TESTING=ON" "-DDOWNLOAD_XTENSOR=OFF") #:phases '(modify-phases %standard-phases @@ -15138,28 +15135,6 @@ used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") (license license:bsd-3)))) -(define-public r-r4rna - (package - (name "r-r4rna") - (version "0.1.4") - (source - (origin - (method url-fetch) - (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" - version ".tar.gz")) - (sha256 - (base32 - "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) - (build-system r-build-system) - (propagated-inputs - (list r-optparse r-rcolorbrewer)) - (home-page "https://www.e-rna.org/r-chie/index.cgi") - (synopsis "Analysis framework for RNA secondary structure") - (description - "The R4RNA package aims to be a general framework for the analysis of RNA -secondary structure and comparative analysis in R.") - (license license:gpl3+))) - (define-public rcas-web (let ((commit "71c93e3835653beb4eaa6e89b860bee3779729b8") (revision "2")) @@ -16252,7 +16227,7 @@ dispersal. Its output can be processed by treeannotator (from the (define-public imp (package (name "imp") - (version "2.15.0") + (version "2.23.0") (source (origin (method url-fetch) @@ -16260,7 +16235,7 @@ dispersal. Its output can be processed by treeannotator (from the version "/download/imp-" version ".tar.gz")) (sha256 (base32 - "05hsrnkpkajppa3f45x4qsarnkj616hlby749zxg4is3bv4i6b5y")))) + "080z50iq1f3nmkccy2i5hj0i34j26sbwcaqizcbljji9mvp0nc0q")))) (build-system cmake-build-system) (arguments `(#:tests? #false ; The test suite is notoriously fickle @@ -16285,6 +16260,7 @@ dispersal. Its output can be processed by treeannotator (from the (list python-wrapper swig)) (inputs (list boost-for-mysql + cereal cgal gsl hdf5 @@ -18845,6 +18821,9 @@ Thus the per-base error rate is similar to the raw input reads.") (build-system qt-build-system) (arguments (list + #:modules '((guix build qt-build-system) + ((guix build gnu-build-system) #:prefix gnu:) + (guix build utils)) ;; TODO: Once <https://issues.guix.gnu.org/47475> is fixed, ;; consider uncommenting the following: ;; @@ -18865,6 +18844,7 @@ Thus the per-base error rate is similar to the raw input reads.") (with-directory-excursion "tests" (setenv "XDG_RUNTIME_DIR" (getcwd)) (invoke "./bandage_command_line_tests.sh"))))) + (replace 'build (assoc-ref gnu:%standard-phases 'build)) (replace 'install (lambda _ (install-file "Bandage" (string-append #$output "/bin"))))))) @@ -23488,8 +23468,7 @@ The output is in SAM format.") "0slkagrk3nfi2qsksv6b1brj6zhx4bj4bkib2sdycvrcd10ql2lh")))) (build-system cmake-build-system) (arguments - `(#:test-target "test" - #:configure-flags + `(#:configure-flags ,#~(list "-DWITH_CHECK=ON" (string-append "-DLIBXML_LIBRARY=" #$(this-package-input "libxml2") @@ -24617,14 +24596,20 @@ both types of files.") (build-system cmake-build-system) (arguments (list - #:test-target "simple_test" + #:modules '((guix build cmake-build-system) + ((guix build gnu-build-system) #:prefix gnu:) + (guix build utils)) #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'fix-tests - (lambda _ - (substitute* "src/megahit" - (("os.path.join\\(script_path, '..'\\)") - "os.path.join(script_path, '../source')"))))))) + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "src/megahit" + (("os.path.join\\(script_path, '..'\\)") + "os.path.join(script_path, '../source')")))) + (replace 'check + (lambda* (#:rest args) + (apply (assoc-ref gnu:%standard-phases 'check) + #:test-target "simple_test" args)))))) (inputs (list python-wrapper zlib)) (home-page "https://www.ncbi.nlm.nih.gov/pubmed/25609793") (synopsis "Meta-genome assembler") @@ -25210,33 +25195,33 @@ module capable of computing base-level alignments for very large sequences.") (outputs '("out" "doc")) (arguments (list + #:test-exclude (string-join (list "TestFileMetaInformation" + "TestElement2" + "TestSCUValidation" + "TestWriter" + "TestAnonymizer4" + "TestPrinter1" + "TestEcho" + ;; The scanner tests depend on TestWriter output. + "TestStrictScanner1" + "TestStrictScanner2_1" + "TestStrictScanner2" + "TestStrictScanner2_2" + "TestFind") + "|") + #:configure-flags + #~(list "-DGDCM_BUILD_TESTING=true" + "-DGDCM_DOCUMENTATION:BOOL=ON" + "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" + (string-append "-DGDCM_INSTALL_DOC_DIR=" + #$output:doc "/share/doc/" #$name)) #:phases #~(modify-phases %standard-phases (add-before 'build 'set-HOME ;; The build spams ‘Fontconfig error: No writable cache ;; directories’ in a seemingly endless loop otherwise. (lambda _ - (setenv "HOME" "/tmp")))) - #:configure-flags - #~(list "-DGDCM_BUILD_TESTING=true" - (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;" - "'TestFileMetaInformation" - "|TestElement2" - "|TestSCUValidation" - "|TestWriter" - "|TestAnonymizer4" - "|TestPrinter1" - "|TestEcho" - ;; The scanner tests depend on TestWriter output - "|TestStrictScanner1" - "|TestStrictScanner2_1" - "|TestStrictScanner2" - "|TestStrictScanner2_2" - "|TestFind'") - "-DGDCM_DOCUMENTATION:BOOL=ON" - "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" - (string-append "-DGDCM_INSTALL_DOC_DIR=" - #$output:doc "/share/doc/" #$name)))) + (setenv "HOME" "/tmp")))))) (native-inputs (list docbook-xsl doxygen graphviz libxslt)) (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page") (synopsis "Grassroots DICOM library") |