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gnu: python-hicexplorer: Update to 3.7.2.
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2. [build-system]: Use pyproject-build-system. [arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a dependency on an unlicensed package; add phase "fix-references"; add phase "run-only-low-mem-tests". [propagated-inputs]: Remove python-configparser and python-six; add python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz, python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn, python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks, python-scikit-learn, and python-tqdm. [native-inputs]: Add graphviz.
This commit is contained in:
Ricardo Wurmus
parent
c3e330cf36
commit
b66b6bdf70
1 changed files with 94 additions and 12 deletions
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@ -13413,7 +13413,7 @@ (define-public python-hicmatrix
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(define-public python-hicexplorer
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(package
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(name "python-hicexplorer")
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(version "2.1.4")
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(version "3.7.2")
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(source
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(origin
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;; The latest version is not available on Pypi.
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@ -13424,32 +13424,114 @@ (define-public python-hicexplorer
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
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(build-system python-build-system)
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"1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))))
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(build-system pyproject-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'loosen-up-requirements
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(lambda _
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(substitute* "setup.py"
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(("==") ">="))
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#t)))))
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(list
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#:test-flags
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'(list "hicexplorer/test/general/"
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"--ignore" "hicexplorer/test/general/test_hicTADClassifier.py"
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"--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py"
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"-k"
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(string-append
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;; Unknown chromosome: ChrX
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"not test_build_matrix_restrictionCutFile_two"
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;; fixture 'keepSelfLigation' not found
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" and not test_build_matrix_restrictionCutFile_six"
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;; ValueError: object dtype is not supported by sparse matrices
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" and not test_hic_transfer_obs_exp_perChromosome"
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;; No KR balancing available
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" and not test_correct_matrix_KR_partial_cool"
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" and not test_correct_matrix_KR_cool"
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" and not test_correct_matrix_KR_H5"))
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#:phases
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#~(modify-phases %standard-phases
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;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23
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(add-after 'unpack 'remove-dependency-on-krbalancing
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(lambda _
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(substitute* "hicexplorer/hicCorrectMatrix.py"
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(("from krbalancing import.*") "")
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(("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent)
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(string-append m "\n"
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indent "log.error('krbalancing not available')\n"
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indent "exit(1)")))
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(substitute* "setup.py"
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(("\"krbalancing >= 0.0.5\",") ""))
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(substitute* "requirements.txt"
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(("krbalancing >= 0.0.5") ""))))
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(add-after 'unpack 'fix-references
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(lambda _
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(let ((site (string-append #$output "/lib/python"
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#$(version-major+minor
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(package-version python))
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"/site-packages")))
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(substitute* "hicexplorer/lib/tadClassifier.py"
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(("model_location = site.getsitepackages\\(\\)\\[0\\]")
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(string-append "model_location = \"" site "\""))))
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(substitute* "hicexplorer/hicFindRestSite.py"
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(("subprocess.check_output\\(\\[\"cat\"")
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(string-append "subprocess.check_output([\""
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(which "cat") "\""))
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(("cmd = 'sort -k1")
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(string-append "cmd = '" (which "sort") " -k1")))))
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;; The tests aim to detect available memory and run more tests when
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;; there is more available memory. Let's run them deterministically
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;; instead and don't run any tests that require more than 1GB of
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;; RAM.
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(add-after 'unpack 'run-only-low-mem-tests
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(lambda _
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(with-directory-excursion "hicexplorer/test"
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(substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_five.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_four.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py"
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"trivial_runs/test_hicBuildMatrix_trivial_runs.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_three.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_two.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py"
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"trivial_runs/test_hicAggregateContacts_trivial_runs_six.py"
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"general/test_hicDifferentialTAD.py"
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"general/test_hicDetectLoops.py"
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"general/test_hicPlotMatrix.py"
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"general/test_hicHyperoptDetectLoops.py"
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"general/test_hicCreateThresholdFile.py"
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"general/test_hicMergeDomains.py"
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"general/test_hicHyperoptDetectLoopsHiCCUPS.py"
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"general/test_hicAggregateContacts.py"
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"general/test_hicInterIntraTAD.py")
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(("^memory =.*") "memory = 1\n"))))))))
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(propagated-inputs
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(list python-biopython
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python-configparser
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python-cleanlab-1
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python-cooler
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python-fit-nbinom
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python-future
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python-graphviz
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python-hic2cool
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python-hicmatrix
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python-hyperopt
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python-imbalanced-learn
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python-intervaltree
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python-ipykernel
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python-jinja2
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python-matplotlib
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python-numpy
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python-pandas
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python-psutil
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python-pybedtools
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python-pybigwig
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python-pygenometracks
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python-pysam
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python-scikit-learn
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python-scipy
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python-six
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python-tables
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python-tqdm
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python-unidecode))
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(native-inputs
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(list graphviz)) ;for hicexplorer/test/test_compute_function.py
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(home-page "https://hicexplorer.readthedocs.io")
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(synopsis "Process, analyze and visualize Hi-C data")
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(description
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