270570f090
gnu: python-snaptools: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable
tests.
Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
2024-01-17 21:41:45 +01:00
9a9f05f1f2
gnu: Add samtools-1.14.
...
* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.
Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
2024-01-16 19:35:37 +01:00
e0369ba57d
gnu: samtools: Update to 1.19.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.
Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
2024-01-16 19:31:35 +01:00
eda31ffaab
gnu: htslib: Update to 1.19.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.
Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
2024-01-16 19:22:03 +01:00
cb1f38cc78
gnu: htscodecs: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0.
Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
2024-01-16 19:17:39 +01:00
f4d2371808
gnu: python-readpaf: Explicitly disable tests.
...
* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.
Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
2024-01-16 14:52:21 +01:00
579b35ddd1
gnu: python-bbknn: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.6.0.
[arguments]: Remove phase 'do-not-fail-to-find-sklearn.
[propagated-inputs]: Add python-pynndescent.
[native-inputs]: Add python-flit-core.
Change-Id: I5fca2d6ca52e54eb7650b3bb24a34a0aa47b1782
2024-01-16 12:44:37 +01:00
076e891754
gnu: python-telomerecat: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests.
Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
2024-01-16 12:44:37 +01:00
65d021a950
gnu: python-scikit-bio: Update to 0.5.9.
...
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7
2024-01-16 12:44:37 +01:00
cda0f029d6
gnu: python-hicexplorer: Make compatible with latest scipy.
...
* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.
Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
2024-01-16 12:44:36 +01:00
3ce25c212f
gnu: python-hicmatrix: Update to 17.1.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1.
[arguments]: Remove.
Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
2024-01-16 12:44:36 +01:00
6b4c911a99
gnu: scvelo: Make compatible with latest matplotlib.
...
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase
'matplotlib-compatibility.
Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
2024-01-16 12:44:36 +01:00
3118d95b56
gnu: python-demuxem: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests,
because there aren't any.
Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
2024-01-16 12:44:36 +01:00
1c01f7e5c6
gnu: python-cooler: Update to 0.9.1.
...
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases; disable tests via #:test-flags.
[propagated-inputs]: Remove python-six and python-sparse.
[native-inputs]: Remove python-codecov, python-mock, and python-pytest-flake8;
add python-coverage, python-hatchling, and python-isort.
Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
2024-01-16 12:44:36 +01:00
3d3a55ec19
gnu: python-plastid: Update to 0.6.1.
...
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1.
[arguments]: Disable four tests.
Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
2024-01-16 12:44:36 +01:00
3a58a3ef05
gnu: cnvkit: Update to 0.9.10.
...
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10.
[arguments]: Remove.
[inputs]: Add r-minimal.
Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
2024-01-16 12:44:36 +01:00
b8e4be02eb
gnu: python-pegasusio: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable
tests.
Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
2024-01-16 12:44:36 +01:00
c620c8ae81
gnu: python-pyani: Disable tests.
...
There are none.
* gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests.
Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
2024-01-16 12:44:35 +01:00
b460f89d93
gnu: tadbit: Add missing input.
...
* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib.
Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
2024-01-16 12:44:35 +01:00
447876fa0d
gnu: python-scanpy: Update to 1.9.6.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.6.
[arguments]: Update test flags.
[native-inputs]: Add python-hatchling, python-hatch-vcs, and
python-pytest-nunit.
Change-Id: I6d4dcd267a076c5697ed103650841f520dc9917f
2024-01-16 12:44:35 +01:00
5960c3cdc4
gnu: Add r-azimuth.
...
* gnu/packages/bioinformatics.scm (r-azimuth): New variable.
Change-Id: I2b0d087378028663ee8d76ced8950f7a9721cb03
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-01-12 12:41:18 +01:00
db75afb4c5
gnu: r-signac: Update to 1.12.0-1.8ecdde2.
...
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.12.0-1.8ecdde2.
Change-Id: Ib852f7a23768383fc62d60577f2aaa893c509317
2024-01-10 18:39:13 +01:00
6688e9f4bd
gnu: Add python-telomerecat.
...
* gnu/packages/bioinformatics.scm (python-telomerecat): New variable.
Change-Id: Ice4cd367cab677466630f44f6900fc38e3be350c
2024-01-10 18:39:13 +01:00
16a277e0a9
gnu: Add python-parabam.
...
* gnu/packages/bioinformatics.scm (python-parabam): New variable.
Change-Id: I66ccf5fd0647f908f1cefd38f0d92e589a81683b
2024-01-10 18:39:13 +01:00
9068dc9f29
gnu: Add bustools.
...
* gnu/packages/bioinformatics.scm (bustools): New variable.
Change-Id: I24a936ad1d630663a41855a833e35fb9caa0155c
2024-01-05 18:21:06 +01:00
cb15b360aa
gnu: Add python-snaptools.
...
* gnu/packages/bioinformatics.scm (python-snaptools): New variable.
Change-Id: I4f4b32cbbb64472e65d2d88184173b6e1a75e8d2
2024-01-05 17:55:17 +01:00
41f0de65b4
gnu: Add trinityrnaseq.
...
* gnu/packages/bioinformatics.scm (trinityrnaseq): New variable.
Change-Id: Ia2c45623576e7e2e51b040b1001b1dd88c1324bb
2024-01-05 17:47:46 +01:00
9476bf8701
gnu: scvelo: Disable two broken tests.
...
* gnu/packages/bioinformatics.scm (scvelo)[build-system]: Use
pyproject-build-system.
[arguments]: Disable test_perfect_fit and test_perfect_fit_2d tests because
they fail with unexpected results; use G-expression.
Change-Id: Ied22a2bc044167012ffaaee15a9626e9f5bccdd5
2024-01-05 15:25:11 +01:00
4f53dff911
gnu: python-hicexplorer: Fix build.
...
* gnu/packages/bioinformatics.scm (python-hicexplorer)[snippet]: Remove
catchall pattern of patch version numbers in setup.py.
2024-01-04 13:38:10 +01:00
f462800002
gnu: Add cpat.
...
* gnu/packages/bioinformatics.scm (cpat): New variable.
Change-Id: I7b3acca1bdec2610d7cdaaf6f96440fe000421dd
2024-01-02 22:47:07 +01:00
8ed9ffedd4
gnu: Add r-sleuth.
...
* gnu/packages/bioinformatics.scm (r-sleuth): New variable.
Change-Id: Ic358945548631fd3ac5de96b2efcf1fd93005898
2024-01-02 21:49:13 +01:00
fb3ac987c9
gnu: Add r-wasabi.
...
* gnu/packages/bioinformatics.scm (r-wasabi): New variable.
Change-Id: I5ce6c47f1fb3b1d5dfedd0977e53cb70ce379077
2024-01-02 21:40:44 +01:00
404c4a5aba
gnu: Add r-projectils.
...
* gnu/packages/bioinformatics.scm (r-projectils): New variable.
Change-Id: Ia975cfcb9c79e59b029c6839dc87b5dcb89bf72a
2024-01-02 10:19:35 +01:00
c8e2b85ed1
gnu: Add r-stacas.
...
* gnu/packages/bioinformatics.scm (r-stacas): New variable.
Change-Id: I258a315465ed88b8013d26a36718250c950aa107
2024-01-02 10:19:35 +01:00
ee0cf3b9ff
gnu: r-seurat-utils: Update to 2.5.0-1.c0374cc.
...
* gnu/packages/bioinformatics.scm (r-seurat-utils): Update to 2.5.0-1.c0374cc.
[propagated-inputs]: Add r-databaselinke-r, r-enhancedvolcano, r-foreach,
r-job, r-magrittr, r-pheatmap, r-plotly, r-qs, r-rstudioapi, and r-tidyverse.
Change-Id: Iea2df8205357e7717c0adec00f6852794817d295
2024-01-01 19:22:11 +01:00
679560ffca
gnu: Add r-databaselinke-r.
...
* gnu/packages/bioinformatics.scm (r-databaselinke-r): New variable.
Change-Id: I0cfcb5b6810b7afebbb9ccb02aafcce05507536c
2024-01-01 19:21:59 +01:00
a4a14ab6d7
gnu: Add lammps-serial.
...
* gnu/packages/bioinformatics.scm (lammps-serial): New variable.
Change-Id: Ifd189a28f423e43ddda8654f758486737eef4a3c
2023-12-25 23:21:07 +01:00
95879674c2
gnu: Add lammps.
...
* gnu/packages/bioinformatics.scm (lammps): New variable.
Change-Id: Ic9745a623300b82b7fb1417437220415305e7332
2023-12-25 19:52:13 +01:00
521247658f
gnu: r-sccustomize: Update to 2.0.1-1.3973745.
...
* gnu/packages/bioinformatics.scm (r-sccustomize): Update to 2.0.1-1.3973745.
Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-12-19 14:44:13 +01:00
93597fc39c
gnu: pyscenic: Update to 0.11.2-1.5f170fd.
...
* gnu/packages/bioinformatics.scm (pyscenic): Update to 0.11.2-1.5f170fd.
[build-system]: Use pyproject-build-system.
[arguments]: Patch setup.py.
[propagated-inputs]: Add python-pyarrow.
Change-Id: I3acd7c921c2c44741c0afd0bbda011f63ed14c42
2023-12-15 16:13:14 +01:00
46b1e717cf
gnu: python-ctxcore: Update to 0.2.0.
...
* gnu/packages/bioinformatics.scm (python-ctxcore): Update to 0.2.0.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Replace python-pyarrow-0.16 with python-pyarrow.
Change-Id: I3f72f9872b438c0a624d23becb5d7828f1986da7
2023-12-15 16:13:14 +01:00
b2aa1d7cd0
gnu: r-readwriter: Update to 1.5.3-1.91373c4.
...
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 1.5.3-1.91373c4.
[propagated-inputs]: Remove r-gdata.
Change-Id: Ice16d3b07d7446ca864fd30e46110c9060b83081
2023-12-15 16:13:14 +01:00
07f85bb057
gnu: r-stringendo: Update to 0.6.0.
...
* gnu/packages/bioinformatics.scm (r-stringendo): Update to 0.6.0.
[propagated-inputs]: Remove r-devtools and r-usethis; add r-clipr.
Change-Id: Iff4a841beb51558ba7d5d8e87ee56e7c3f2b2710
2023-12-15 16:13:14 +01:00
4d92caef51
gnu: r-liana: Add missing inputs.
...
* gnu/packages/bioinformatics.scm (r-liana)[propagated-inputs]: Add r-basilisk
and r-basilisk-utils.
Change-Id: I5dce058a446245e6797cca1c35485f38b3da819a
2023-12-15 16:13:14 +01:00
951a1433f3
gnu: Add r-illuminahumanmethylationepicmanifest.
...
* gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicmanifest): New variable.
Change-Id: I9635033ed5e7e44ecfaff76cd002379582900686
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-13 14:46:51 +01:00
4c17016019
gnu: Add r-ewastools.
...
* gnu/packages/bioinformatics.scm (r-ewastools): New variable.
Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 17:03:24 +01:00
e16d152463
gnu: Add r-dnamcrosshyb.
...
* gnu/packages/bioinformatics.scm (r-dnamcrosshyb): New variable.
Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04 16:30:11 +01:00
b30127052e
gnu: r-readwriter: Update to 0.3.2-1.12d32cb.
...
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb.
Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
2023-11-03 22:49:28 +01:00
c9361460de
gnu: Add r-miamiplot.
...
* gnu/packages/bioinformatics.scm (r-miamiplot): New variable.
Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03 14:10:13 +01:00
b963bf6b1d
gnu: python-baltica: Add missing R inputs.
...
* gnu/packages/bioinformatics.scm (python-baltica)[propagated-inputs]: Add
r-biocmanager, r-dplyr, r-genomicranges, r-here, r-openxlsx, r-optparse,
r-readr, r-rsamtools, r-stringr, r-tidyr, r-upsetr, and r-yaml.
[description]: Add an extra space after a period.
Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676
2023-10-31 22:03:24 +01:00
Ricardo Wurmus
nafkhamdc
Troy Figiel
Mădălin Ionel Patrașcu