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3692 Commits

Author SHA1 Message Date
Ricardo Wurmus
391b612d0a
gnu: r-archr: Update to 1.0.2-1.c61b064. 
* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.2-1.c61b064.

Change-Id: I8967cedbfc3390c364f188d50f8ecb2b27cb1417
 2024-02-19 13:37:14 +01:00
nafkhamdc
07ecdb99b6
gnu: python-ega-download-client: Add missing input. 
* gnu/packages/bioinformatics.scm (python-ega-download-client)
[native-inputs]: Add python-mock.

Change-Id: I3befca6de33f959f4d916caa839d7201c77e8209
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-02-19 10:13:41 +01:00
nafkhamdc
fb79e58995
gnu: Add python-ega-download-client. 
* gnu/packages/bioinformatics.scm (python-ega-download-client): New variable.

Change-Id: I3233774975989f912281ab2e6ec6ad3362cae18b
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-02-15 11:53:29 +01:00
Sharlatan Hellseher
c185c51e14
gnu: go-github.com-ulikunitz-xz: Move to golang-compression. 
* gnu/packages/golang.scm (go-github.com-ulikunitz-xz): Move from here ...
* gnu/packages/golang-compression.scm: ... to here.

* gnu/packages/admin.scm: Add (gnu packages golang-compression) module.
* gnu/packages/bioinformatics.scm: As above.

Change-Id: I1901e67ac4336efd356085332572b3f09de90f7a
 2024-02-13 14:33:17 +00:00
Sharlatan Hellseher
de36ec1480
gnu: go-golang-org-x-text: Move to golang-build. 
* gnu/packages/golang.scm (go-golang-org-x-text): Move from here ...
* gnu/packages/golang-build.scm: ... to here.

* gnu/packages/admin.scm: Add (gnu packages golang-build) module.
* gnu/packages/bioinformatics.scm: As above.
* gnu/packages/mail.scm: As above.

Change-Id: Ifd15b35b460ae30c5c1d677551e95842b322b246
 2024-02-13 14:33:16 +00:00
nafkhamdc
ca4c9062c4
gnu: Add python-pdbfixer. 
* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.

Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-02-10 11:21:21 +01:00
Arun Isaac
4671925528
gnu: ccwl: Update to 0.3.0. 
* gnu/packages/bioinformatics.scm (ccwl): Update to 0.3.0.
[arguments]: Add patch-more-source-shebangs phase.

Change-Id: Ic7926d04c28eeafd799deba5e817574663431db8
 2024-01-26 15:31:56 +00:00
Ricardo Wurmus
6623a8151a
gnu: Add music. 
* gnu/packages/bioinformatics.scm (music): New variable.

Change-Id: Iba5c986a0d3143118d4640d3ee9d4dae8119163f
 2024-01-25 15:13:51 +01:00
Ricardo Wurmus
c376298c7c
gnu: Add flash. 
* gnu/packages/bioinformatics.scm (flash): New variable.

Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
 2024-01-23 23:47:31 +01:00
Ricardo Wurmus
825b3ca763
gnu: Add isolator. 
* gnu/packages/bioinformatics.scm (isolator): New variable.

Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
 2024-01-23 23:43:19 +01:00
Ricardo Wurmus
b9a5c50d8c
gnu: Add metal. 
* gnu/packages/bioinformatics.scm (metal): New variable.

Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
 2024-01-23 21:41:58 +01:00
Ricardo Wurmus
25f0964c3e
gnu: Add randfold. 
* gnu/packages/bioinformatics.scm (randfold): New variable.

Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
 2024-01-23 21:31:51 +01:00
Ricardo Wurmus
ebad9d6c0e
gnu: Add python-pyfasta. 
* gnu/packages/bioinformatics.scm (python-pyfasta): New variable.

Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
 2024-01-23 21:26:50 +01:00
Ricardo Wurmus
f7373261e9
gnu: Add python-fcsparser. 
* gnu/packages/bioinformatics.scm (python-fcsparser): New variable.

Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
 2024-01-23 21:22:45 +01:00
Ricardo Wurmus
469405375c
gnu: Add lsgkm. 
* gnu/packages/bioinformatics.scm (lsgkm): New variable.

Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
 2024-01-23 21:18:07 +01:00
Ricardo Wurmus
d3129b3f1e
gnu: Add eddylab-squid. 
* gnu/packages/bioinformatics.scm (eddylab-squid): New variable.

Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
 2024-01-23 13:52:36 +01:00
Ricardo Wurmus
6a82745746
gnu: Add python-magic-impute. 
* gnu/packages/bioinformatics.scm (python-magic-impute): New variable.

Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
 2024-01-23 13:42:55 +01:00
Ricardo Wurmus
6e835cd380
gnu: Add r-scenic. 
* gnu/packages/bioinformatics.scm (r-scenic): New variable.

Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
 2024-01-23 13:36:47 +01:00
Arun Isaac
4987618368
gnu: wfmash: Update to 0.12.5. 
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5.
(source): Use git-fetch. Update git repository URL.
(arguments): In check phase, symlink to "../source/data" and change wfmash
invocation arguments.
(home-page): Update URL.

Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72
 2024-01-19 18:04:39 +00:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
nafkhamdc
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
nafkhamdc
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
Ricardo Wurmus
6688e9f4bd
gnu: Add python-telomerecat. 
* gnu/packages/bioinformatics.scm (python-telomerecat): New variable.

Change-Id: Ice4cd367cab677466630f44f6900fc38e3be350c
 2024-01-10 18:39:13 +01:00
Ricardo Wurmus
16a277e0a9
gnu: Add python-parabam. 
* gnu/packages/bioinformatics.scm (python-parabam): New variable.

Change-Id: I66ccf5fd0647f908f1cefd38f0d92e589a81683b
 2024-01-10 18:39:13 +01:00
Ricardo Wurmus
9068dc9f29
gnu: Add bustools. 
* gnu/packages/bioinformatics.scm (bustools): New variable.

Change-Id: I24a936ad1d630663a41855a833e35fb9caa0155c
 2024-01-05 18:21:06 +01:00
Ricardo Wurmus
cb15b360aa
gnu: Add python-snaptools. 
* gnu/packages/bioinformatics.scm (python-snaptools): New variable.

Change-Id: I4f4b32cbbb64472e65d2d88184173b6e1a75e8d2
 2024-01-05 17:55:17 +01:00
Ricardo Wurmus
41f0de65b4
gnu: Add trinityrnaseq. 
* gnu/packages/bioinformatics.scm (trinityrnaseq): New variable.

Change-Id: Ia2c45623576e7e2e51b040b1001b1dd88c1324bb
 2024-01-05 17:47:46 +01:00
Ricardo Wurmus
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
Troy Figiel
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
Ricardo Wurmus
f462800002
gnu: Add cpat. 
* gnu/packages/bioinformatics.scm (cpat): New variable.

Change-Id: I7b3acca1bdec2610d7cdaaf6f96440fe000421dd
 2024-01-02 22:47:07 +01:00
Ricardo Wurmus
8ed9ffedd4
gnu: Add r-sleuth. 
* gnu/packages/bioinformatics.scm (r-sleuth): New variable.

Change-Id: Ic358945548631fd3ac5de96b2efcf1fd93005898
 2024-01-02 21:49:13 +01:00