diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 59 |
1 files changed, 42 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56e207fbd4..5adbbdd42f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6536,31 +6536,56 @@ Cuffdiff or Ballgown programs.") (define-public taxtastic (package (name "taxtastic") - (version "0.8.5") + (version "0.8.11") (source (origin - (method url-fetch) - (uri (pypi-uri "taxtastic" version)) + ;; The Pypi version does not include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/fhcrc/taxtastic.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk")))) + "1sv8mkg64jn7zdwf1jj71c16686yrwxk0apb1l8sjszy9p166g0p")))) (build-system python-build-system) (arguments - `(#:python ,python-2 - #:phases + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'prepare-directory + (lambda _ + ;; The git checkout must be writable for tests. + (for-each make-file-writable (find-files ".")) + ;; This test fails, but the error is not caught by the test + ;; framework, so the tests fail... + (substitute* "tests/test_taxit.py" + (("self.cmd_fails\\(''\\)") + "self.cmd_fails('nothing')")) + ;; This version file is expected to be created with git describe. + (mkdir-p "taxtastic/data") + (with-output-to-file "taxtastic/data/ver" + (lambda () (display ,version))) + #t)) + (add-after 'unpack 'python37-compatibility + (lambda _ + (substitute* "taxtastic/utils.py" + (("import csv") "import csv, errno") + (("os.errno") "errno")) + #t)) (replace 'check - (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))))) + ;; Note, this fails to run with "-v" as it tries to write to a + ;; closed output stream. + (lambda _ (invoke "python" "-m" "unittest") #t))))) (propagated-inputs - `(("python-sqlalchemy" ,python2-sqlalchemy) - ("python-decorator" ,python2-decorator) - ("python-biopython" ,python2-biopython) - ("python-pandas" ,python2-pandas) - ("python-psycopg2" ,python2-psycopg2) - ("python-fastalite" ,python2-fastalite) - ("python-pyyaml" ,python2-pyyaml) - ("python-six" ,python2-six) - ("python-jinja2" ,python2-jinja2) - ("python-dendropy" ,python2-dendropy))) + `(("python-sqlalchemy" ,python-sqlalchemy) + ("python-decorator" ,python-decorator) + ("python-biopython" ,python-biopython) + ("python-pandas" ,python-pandas) + ("python-psycopg2" ,python-psycopg2) + ("python-fastalite" ,python-fastalite) + ("python-pyyaml" ,python-pyyaml) + ("python-six" ,python-six) + ("python-jinja2" ,python-jinja2) + ("python-dendropy" ,python-dendropy))) (home-page "https://github.com/fhcrc/taxtastic") (synopsis "Tools for taxonomic naming and annotation") (description |