diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 218 |
1 files changed, 47 insertions, 171 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 69484bbb64..8dffc86c00 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7270,8 +7270,6 @@ 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"))) @@ -7325,7 +7323,7 @@ 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 @@ -11369,7 +11367,6 @@ 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 @@ -12327,7 +12324,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (define-public sortmerna (package (name "sortmerna") - (version "4.3.4") + (version "4.3.7") (source (origin (method git-fetch) @@ -12337,7 +12334,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (file-name (git-file-name name version)) (sha256 (base32 - "0f8jfc8vsq6llhbb92p9yv7nbp566yqwfcmq3g2hw0n7d8hyl3a8")))) + "14p3zi6ysnrs2l33r5mc0fr0la2jnnxmqdcif02fppln8w31j753")))) (build-system cmake-build-system) (outputs '("out" ;for binaries "db")) ;for sequence databases @@ -12362,6 +12359,11 @@ of these reads to align data quickly through a hash-based indexing scheme.") "/include")) #:phases '(modify-phases %standard-phases + (add-after 'unpack 'fix-includes + (lambda _ + (substitute* "src/sortmerna/kseq_load.cpp" + (("#include <iostream>" all) + (string-append all "\n#include <cstdint>"))))) (add-after 'unpack 'find-concurrentqueue-headers (lambda* (#:key inputs #:allow-other-keys) ;; Ensure that headers can be found @@ -18823,6 +18825,9 @@ 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: ;; @@ -18843,6 +18848,7 @@ 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"))))))) @@ -20391,141 +20397,6 @@ includes operations like compartment, insulation or peak calling.") the HiCExplorer and pyGenomeTracks packages.") (license license:gpl3+))) -(define-public python-hicexplorer - (package - (name "python-hicexplorer") - (version "3.7.4") - (source - (origin - ;; The latest version is not available on Pypi. - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/HiCExplorer") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1cjr9l0vcngd0f4dmar388ri1ah1bqybnn53jc85xwh07wfacq7l")))) - (build-system pyproject-build-system) - (arguments - (list - #:test-flags - '(list "hicexplorer/test/general/" - "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py" - "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py" - "-k" - (string-append - ;; Unknown chromosome: ChrX - "not test_build_matrix_restrictionCutFile_two" - ;; fixture 'keepSelfLigation' not found - " and not test_build_matrix_restrictionCutFile_six" - ;; ValueError: object dtype is not supported by sparse matrices - " and not test_hic_transfer_obs_exp_perChromosome" - - ;; No KR balancing available - " and not test_correct_matrix_KR_partial_cool" - " and not test_correct_matrix_KR_cool" - " and not test_correct_matrix_KR_H5")) - #:phases - #~(modify-phases %standard-phases - ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23 - (add-after 'unpack 'remove-dependency-on-krbalancing - (lambda _ - (substitute* "hicexplorer/hicCorrectMatrix.py" - (("from krbalancing import.*") "") - (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent) - (string-append m "\n" - indent "log.error('krbalancing not available')\n" - indent "exit(1)"))) - (substitute* "setup.py" - (("\"krbalancing >= 0.0.5\",") "")) - (substitute* "requirements.txt" - (("krbalancing >= 0.0.5") "")))) - (add-after 'unpack 'fix-references - (lambda _ - (let ((site (string-append #$output "/lib/python" - #$(version-major+minor - (package-version python)) - "/site-packages"))) - (substitute* "hicexplorer/lib/tadClassifier.py" - (("model_location = site.getsitepackages\\(\\)\\[0\\]") - (string-append "model_location = \"" site "\"")))) - (substitute* "hicexplorer/hicFindRestSite.py" - (("subprocess.check_output\\(\\[\"cat\"") - (string-append "subprocess.check_output([\"" - (which "cat") "\"")) - (("cmd = 'sort -k1") - (string-append "cmd = '" (which "sort") " -k1"))))) - ;; The tests aim to detect available memory and run more tests when - ;; there is more available memory. Let's run them deterministically - ;; instead and don't run any tests that require more than 1GB of - ;; RAM. - (add-after 'unpack 'run-only-low-mem-tests - (lambda _ - (with-directory-excursion "hicexplorer/test" - (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py" - "trivial_runs/test_hicBuildMatrix_trivial_runs.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py" - "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py" - "general/test_hicDifferentialTAD.py" - "general/test_hicDetectLoops.py" - "general/test_hicPlotMatrix.py" - "general/test_hicHyperoptDetectLoops.py" - "general/test_hicCreateThresholdFile.py" - "general/test_hicMergeDomains.py" - "general/test_hicHyperoptDetectLoopsHiCCUPS.py" - "general/test_hicAggregateContacts.py" - "general/test_hicInterIntraTAD.py") - (("^memory =.*") "memory = 1\n")))))))) - (propagated-inputs - (list python-biopython - python-cleanlab - python-cooler - python-fit-nbinom - python-future - python-graphviz - python-hic2cool - python-hicmatrix - python-hyperopt - python-imbalanced-learn - python-intervaltree - python-ipykernel - python-jinja2 - python-matplotlib - python-numpy - python-pandas - python-psutil - python-pybedtools - python-pybigwig - python-pygenometracks - python-pysam - python-scikit-learn - python-scipy - python-tables - python-tqdm - python-unidecode)) - (native-inputs - (list graphviz)) ;for hicexplorer/test/test_compute_function.py - (home-page "https://hicexplorer.readthedocs.io") - (synopsis "Process, analyze and visualize Hi-C data") - (description - "HiCExplorer is a powerful and easy to use set of tools to process, -normalize and visualize Hi-C data. HiCExplorer facilitates the creation of -contact matrices, correction of contacts, TAD detection, A/B compartments, -merging, reordering or chromosomes, conversion from different formats -including cooler and detection of long-range contacts. Moreover, it allows -the visualization of multiple contact matrices along with other types of data -like genes, compartments, ChIP-seq coverage tracks (and in general any type of -genomic scores), long range contacts and the visualization of viewpoints.") - (license license:gpl3))) - (define-public python-pygenometracks (package (name "python-pygenometracks") @@ -23466,8 +23337,7 @@ 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=" #$(this-package-input "libxml2") @@ -24595,14 +24465,20 @@ both types of files.") (build-system cmake-build-system) (arguments (list - #:test-target "simple_test" + #:modules '((guix build cmake-build-system) + ((guix build gnu-build-system) #:prefix gnu:) + (guix build utils)) #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'fix-tests - (lambda _ - (substitute* "src/megahit" - (("os.path.join\\(script_path, '..'\\)") - "os.path.join(script_path, '../source')"))))))) + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "src/megahit" + (("os.path.join\\(script_path, '..'\\)") + "os.path.join(script_path, '../source')")))) + (replace 'check + (lambda* (#:rest args) + (apply (assoc-ref gnu:%standard-phases 'check) + #:test-target "simple_test" args)))))) (inputs (list python-wrapper zlib)) (home-page "https://www.ncbi.nlm.nih.gov/pubmed/25609793") (synopsis "Meta-genome assembler") @@ -25188,33 +25064,33 @@ module capable of computing base-level alignments for very large sequences.") (outputs '("out" "doc")) (arguments (list + #:test-exclude (string-join (list "TestFileMetaInformation" + "TestElement2" + "TestSCUValidation" + "TestWriter" + "TestAnonymizer4" + "TestPrinter1" + "TestEcho" + ;; The scanner tests depend on TestWriter output. + "TestStrictScanner1" + "TestStrictScanner2_1" + "TestStrictScanner2" + "TestStrictScanner2_2" + "TestFind") + "|") + #:configure-flags + #~(list "-DGDCM_BUILD_TESTING=true" + "-DGDCM_DOCUMENTATION:BOOL=ON" + "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" + (string-append "-DGDCM_INSTALL_DOC_DIR=" + #$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") |