@@ 20397,141 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")