diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 22 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 862eb31364..eac62ffcc1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3330,10 +3330,7 @@ and gene expression visualization.") python-scipy python-threadpoolctl python-umap-learn)) - (native-inputs (list python-pytest - python-setuptools - python-sphinx - python-sphinx-rtd-theme)) + (native-inputs (list python-pytest python-setuptools)) (home-page "https://github.com/tanaylab/metacells.git") (synopsis "Single-cell RNA Sequencing Analysis") (description "The metacells package implements the improved metacell @@ -3359,8 +3356,7 @@ cells).") (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z")))) (build-system pyproject-build-system) (propagated-inputs (list python-ete3 python-numpy python-six)) - (native-inputs (list python-black python-flake8 python-pytest python-twine - python-wheel)) + (native-inputs (list python-pytest)) (home-page "https://github.com/tresoldi/ngesh") (synopsis "Library for phylogenetic tree simulation") (description @@ -8289,19 +8285,18 @@ average nucleotide identity.") (define-public python-pyahocorasick (package (name "python-pyahocorasick") - (version "2.1.0") + (version "2.2.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/WojciechMula/pyahocorasick") - (commit version))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1fsnivwcw56q7lwz41c5kbfvxv0v17mmkx43i2a293l49fxj08j8")))) + (base32 "0r9n8awy80dg8dmgza4kpgwbpkvjf4s85cyswnq04h3x6cf62lll")))) (build-system pyproject-build-system) - (native-inputs (list python-pytest python-twine python-setuptools - python-wheel)) + (native-inputs (list python-pytest python-setuptools)) (home-page "https://github.com/WojciechMula/pyahocorasick") (synopsis "Library for finding multiple key strings in text") (description @@ -22323,19 +22318,19 @@ multiple experimental contexts.") (define-public vbz-compression (package (name "vbz-compression") - (version "1.0.3") + (version "1.0.13") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/nanoporetech/vbz_compression/") - (commit (string-append "v" version)) + (commit version) ;; We include the streamvbyte sources (recursive? #true))) (file-name (git-file-name name version)) (sha256 (base32 - "1rn5d98flvjblhj4zjpcdqqh8qlgsh5cmb13i49fnm187p03097z")))) + "1jf5i5v0h58s7w6rhgi4w1vvxnk9jzbgmiic14d48ngr204m0w5c")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -22365,8 +22360,8 @@ effective when applied to the signal dataset.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nanoporetech/ont_fast5_api") - (commit (string-append "release_" version)))) + (url "https://github.com/nanoporetech/ont_fast5_api") + (commit (string-append "release_" version)))) (file-name (git-file-name name version)) (sha256 (base32 @@ -22376,15 +22371,17 @@ effective when applied to the signal dataset.") '(delete-file-recursively "ont_fast5_api/vbz_plugin")))) (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'copy-plugin - (lambda* (#:key inputs #:allow-other-keys) - (mkdir-p "ont_fast5_api/vbz_plugin/") - (install-file (string-append - (assoc-ref inputs "vbz-compression") - "/hdf5/lib/plugin/libvbz_hdf_plugin.so") - "ont_fast5_api/vbz_plugin/")))))) + (list + #:test-backend #~'unittest + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'copy-plugin + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "ont_fast5_api/vbz_plugin/") + (install-file (string-append + #$(this-package-input "vbz-compression") + "/hdf5/lib/plugin/libvbz_hdf_plugin.so") + "ont_fast5_api/vbz_plugin/")))))) (inputs (list vbz-compression)) (propagated-inputs |