c9892edceb
gnu: biobambam2: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to
%build-inputs by using a gexp.
2021-12-05 15:04:02 +01:00
a8b60bd475
gnu: sjcount: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to
%build-inputs by using a gexp.
2021-12-05 15:04:02 +01:00
4c6cb448fd
gnu: sjcount: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T
from build phases.
2021-12-05 15:04:02 +01:00
c1fe074915
gnu: dropseq-tools: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference
to %build-inputs by using a gexp.
2021-12-05 15:04:02 +01:00
1462e5c919
gnu: dropseq-tools: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove
trailing #T from build phases...
[source]: ...and from the snippet.
2021-12-05 15:04:02 +01:00
10554e0a57
gnu: python-django-netfields: Update to 1.2.4.
...
* gnu/packages/django.scm (python-django-netfields): Update to 1.2.4.
2021-12-05 14:40:08 +01:00
50fff94b5a
gnu: python-django: Update to 3.2.9.
...
* gnu/packages/django.scm (python-django): Update to 3.2.9.
2021-12-05 14:40:08 +01:00
e166e6acf6
gnu: drbd-utils: Update to 9.19.1.
...
* gnu/packages/cluster.scm (drbd-utils): Update to 9.19.1.
2021-12-05 14:40:07 +01:00
21e2be5968
gnu: emacs-peg: Update to 0.10.3.
...
* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3.
2021-12-05 14:20:16 +01:00
c61e49aa94
gnu: tbb: Update to 2021.4.0.
...
* gnu/packages/tbb.scm (tbb): Update to 2021.4.0.
2021-12-05 14:02:10 +01:00
db5646d957
gnu: Adjust for python-build-system behavior change.
...
Commit cb72f9a773
2021-12-05 14:02:10 +01:00
b507cc49ab
gnu: python-pyvcf: Fix bytecode compilation.
...
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to
patch sample script.
2021-12-05 14:02:10 +01:00
a2584a08be
gnu: python-whisper: Update to 1.1.8.
...
* gnu/packages/monitoring.scm (python-whisper): Update to 1.1.8.
2021-12-05 14:02:10 +01:00
0d196ab9bd
gnu: python-mailman-hyperkitty: Update to 1.2.0.
...
* gnu/packages/mail.scm (python-mailman-hyperkitty): Update to 1.2.0.
[source](patches): Remove.
2021-12-05 14:02:10 +01:00
3f9d122dcb
gnu: python-hyperkitty: Update to 1.3.5.
...
* gnu/packages/mail.scm (python-hyperkitty): Update to 1.3.5.
[arguments]: Add pythonpath in test invokation.
[propagated-inputs]: Add PYTHON-MISTUNE-NEXT. Change from PYTHON-DJANGO-2.2
to PYTHON-DJANGO.
[native-inputs]: Add PYTHON-LXML.
2021-12-05 14:02:10 +01:00
b0ce8bdb39
gnu: Add python-mistune-next.
...
* gnu/packages/python-xyz.scm (python-mistune-next): New variable.
2021-12-05 14:02:09 +01:00
f457fb19dd
gnu: python-django-haystack: Update to 3.1.1.
...
* gnu/packages/django.scm (python-django-haystack): Update to 3.1.1.
[arguments]: Adjust substitution.
2021-12-05 14:02:09 +01:00
eb8619a5a6
gnu: python-alembic: Update to 1.7.5.
...
* gnu/packages/databases.scm (python-alembic): Update to 1.7.5.
[propagated-inputs]: Remove PYTHON-IMPORTLIB-RESOURCES.
2021-12-05 14:02:09 +01:00
d801827b84
gnu: ganeti: Add the output directory on GUIX_PYTHONPATH.
...
This is a follow-up to commit 1ed567c872
2021-12-05 14:02:09 +01:00
846bd3d083
gnu: python-webassets: Patch for Python 3.9.
...
* gnu/packages/python-web.scm (python-webassets)[arguments]: Add
substitution.
2021-12-05 14:02:09 +01:00
9f5b9d18d8
gnu: python-django-mailman3: Update to 1.3.7.
...
* gnu/packages/mail.scm (python-django-mailman3): Update to 1.3.7.
2021-12-05 14:02:09 +01:00
837688e505
gnu: python-mailmanclient: Update to 3.3.3.
...
* gnu/packages/mail.scm (python-mailmanclient): Update to 3.3.3.
2021-12-05 14:02:09 +01:00
97edcf2e63
gnu: python-django-url-filter: Adjust phase order.
...
* gnu/packages/django.scm (python-django-url-filter)[arguments]: Move
substitution to after the unpack phase, so that it does not end up in the egg
info.
2021-12-05 14:02:09 +01:00
458e972484
gnu: python-django-netfields: Propagate psycopg2.
...
* gnu/packages/django.scm (python-django-netfields)[propagated-inputs]: Add
PYTHON-PSYCOPG2.
2021-12-05 14:02:09 +01:00
63975ea51c
gnu: python-django-logging-json: Disable sanity check.
...
* gnu/packages/django.scm (python-django-logging-json)[arguments]: Add
#:phases.
2021-12-05 14:02:09 +01:00
19520996f0
gnu: python-django-appconf: Fix tests.
...
* gnu/packages/django.scm (python-django-appconf): Invoke django-admin with
custom pythonpath.
2021-12-05 14:02:09 +01:00
88e9e9e697
gnu: python-django-pipeline: Fix tests.
...
* gnu/packages/django.scm (python-django-pipeline): Provide pythonpath to
django-admin.
2021-12-05 14:02:09 +01:00
e73f565445
gnu: python-django-sortedm2m: Fix tests.
...
This is a follow-up to commit 283d5ac97f
2021-12-05 14:02:08 +01:00
ddea9e32e7
gnu: python-django-contact-form: Update to 1.9.
...
* gnu/packages/django.scm (python-django-contact-form): Update to 1.9.
2021-12-05 14:02:08 +01:00
6b458747da
gnu: python-django-jinja: Update to 2.9.1.
...
* gnu/packages/django.scm (python-django-jinja): Update to 2.9.1.
2021-12-05 14:02:08 +01:00
de5a8b26f2
gnu: python-django-haystack: Disable sanity check.
...
* gnu/packages/django.scm (python-django-haystack)[arguments]: Delete one
phase. While at it, remove trailing #t's.
2021-12-05 14:02:08 +01:00
acbc01940b
gnu: python-fakeredis: Update to 1.7.0.
...
* gnu/packages/databases.scm (python-fakeredis): Update to 1.7.0.
2021-12-05 14:02:08 +01:00
0b6f4be0fa
gnu: Django packages propagate Django, after all.
...
This reverts commit d7922f488b
2021-12-05 14:02:08 +01:00
bf9a1dfd59
gnu: Add imppg
...
* gnu/packages/astronomy.scm: (imppg): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 12:35:55 +01:00
c663d037aa
gnu: Add pqiv.
...
* gnu/packages/image-viewers.scm (pqiv): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 12:27:02 +01:00
66a2d3830c
gnu: Add pudb.
...
* gnu/packages/python-xyz.scm (pudb): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 12:18:24 +01:00
53afb3cf2a
gnu: leo: Use GIT-VERSION.
...
* gnu/packages/web-browsers.scm (leo)[source]: Use `git-version' instead of
crafting version string. Also fix indentation.
2021-12-05 12:08:16 +01:00
2149515808
gnu: Add leo.
...
* gnu/packages/web-browsers.scm (leo): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-05 11:03:14 +01:00
e70e26423b
gnu: minimap2: Update to 2.23.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
2021-12-05 11:51:10 +02:00
030d9b261f
gnu: Add guile-ini.
...
* gnu/packages/guile-xyz.scm (guile-ini): New variable.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-05 09:53:59 +01:00
f8490817e7
gnu: evolution: Build with libsoup 2.
...
* gnu/packages/gnome.scm (evolution) [phase adjust-webkitgtk-version]: Remove
it.
[inputs]: Depend on webkitgtk-with-libsoup2 instead of webkitgtk.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-05 08:42:03 +01:00
7e6ee16d49
gnu: tla2tools: Remove reference to %output.
...
* gnu/packages/java.scm (tla2tools)[arguments]: Bind OUTPUTS in build phase
'install to remove reference to %output.
2021-12-05 01:11:38 +01:00
ad1dc0cad3
gnu: java-log4j-core: Remove reference to %outputs.
...
* gnu/packages/java.scm (java-log4j-core)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-05 01:04:29 +01:00
87e7ed77da
gnu: java-log4j-api: Remove reference to %outputs.
...
* gnu/packages/java.scm (java-log4j-api)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-05 01:04:03 +01:00
9485578570
gnu: java-native-access: Use older GCC.
...
* gnu/packages/java.scm (java-native-access)[native-inputs]: Add gcc-7 to fix
the build.
2021-12-05 01:03:31 +01:00
48235c37db
gnu: java-commons-math3: Remove trailing #T.
...
* gnu/packages/java.scm (java-commons-math3)[arguments]: Remove trailing #T
from build phase.
2021-12-05 00:49:06 +01:00
1e7bd5e679
gnu: salmon: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove
reference to %build-inputs.
2021-12-05 00:49:06 +01:00
20d525a842
gnu: Add libphonenumber
...
* gnu/package/messaging.scm (libphonenumber): New variable
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2021-12-04 23:03:54 +01:00
ac872546fc
gnu: Add guile-smc
...
* gnu/packages/guile-xyz.scm (guile-smc): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-12-04 22:45:27 +01:00
3ee142ebd6
gnu: libhandy: Skip test that requires librsvg on non-x86_64.
...
* gnu/packages/gnome.scm (libhandy)[arguments]: Add
'skip-test-that-requires-svg' phase on non-x86_64.
2021-12-04 22:39:47 +01:00
73f78d556b
gnu: gtranslator: Update to 40.0.
...
* gnu/packages/gnome.scm (gtranslator): Update to 40.0.
[inputs]: Add LIBHANDY.
2021-12-04 22:39:46 +01:00
d4c4348d83
gnu: gtranslator: Fix compilation.
...
* gnu/packages/gnome.scm (gtranslator)[inputs]: Replace LIBSOUP with
LIBSOUP-MINIMAL-2.
[arguments]: Pass #:meson.
2021-12-04 22:39:46 +01:00
3f03f502ee
gnu: libgda: Do not use the bundled sqlite.
...
* gnu/packages/gnome.scm (libgda)[source]: Add snippet.
[arguments]: Pass "--enable-system-sqlite".
[inputs]: Add SQLITE.
2021-12-04 22:39:46 +01:00
634b46a469
gnu: java-commons-math3: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-math3)[arguments]: Use a gexp
to remove references to %build-inputs.
2021-12-04 22:07:26 +01:00
ba5cb6456d
gnu: java-commons-collections4: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-collections4)[arguments]: Use a gexp
to remove references to %build-inputs.
2021-12-04 22:07:17 +01:00
035fec27fc
gnu: java-commons-exec-1.1: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-exec-1.1)[arguments]: Use a gexp
to remove references to %build-inputs.
2021-12-04 22:07:11 +01:00
5a4ad372ef
gnu: java-commons-exec: Remove references to %build-inputs.
...
* gnu/packages/java.scm (java-commons-exec)[arguments]: Use a gexp to
remove references to %build-inputs.
2021-12-04 22:06:49 +01:00
2aee138485
gnu: maven-components-parent-pom-22: Remove references to %build-inputs.
...
* gnu/packages/maven-parent-pom.scm (maven-components-parent-pom-22)
[arguments]: Use a gexp to remove references to %build-inputs.
2021-12-04 22:06:41 +01:00
d29f14aca2
gnu: java-sonatype-oss-parent-pom-9: Remove references to %build-inputs.
...
* gnu/packages/maven-parent-pom.scm (java-sonatype-oss-parent-pom-9)
[arguments]: Use a gexp to remove references to %build-inputs.
2021-12-04 22:06:23 +01:00
f044ffc1c4
gnu: ocaml4.07-ppx-let: Make 'properties' an alist.
...
The incorrect 'properties' value was introduced in
3649c56a5f
2021-12-04 21:57:27 +01:00
98d2abe523
gnu: sailfish: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove
references to %build-inputs.
2021-12-04 19:54:28 +01:00
39e2a84f52
gnu: sailfish: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from
snippet.
2021-12-04 19:54:28 +01:00
b0fd09f856
gnu: piranha: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove
references to %build-inputs.
2021-12-04 19:54:28 +01:00
01d2e2b334
gnu: piranha: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T
from build phases.
2021-12-04 19:54:28 +01:00
502538c6e4
gnu: emboss: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove
reference to %build-inputs.
2021-12-04 19:54:28 +01:00
2657bdc100
gnu: vcftools: Replace references to %outputs.
...
* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove
references to %outputs.
2021-12-04 19:54:28 +01:00
eec1bdcd9e
gnu: seqan-1: Use gexp for builder.
...
* gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
2021-12-04 19:54:28 +01:00
2c1c75a56c
gnu: seqan-2: Use gexp for builder.
...
* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove
references to %build-inputs and %outputs.
2021-12-04 19:54:28 +01:00
f41576c09f
gnu: sra-tools: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead
of referencing %build-inputs.
2021-12-04 19:54:27 +01:00
f33e490334
gnu: preseq: Remove references to %outputs and %build-inputs.
...
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to
%outputs and %build-inputs by using a gexp.
2021-12-04 19:54:27 +01:00
8a446f5e41
gnu: preseq: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet.
2021-12-04 19:54:27 +01:00
bd746917a2
gnu: julia-forwarddiff: Disable tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-forwarddiff)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:33 +02:00
82586916be
gnu: julia-geometrybasics: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz (julia-geometrybasics)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:33 +02:00
eb4f1fcf74
gnu: julia-structarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-structarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in the test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
afd35e8e9c
gnu: julia-mutablearithmetics: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-mutablearithmetics)[arguments]<#:phases>:
Conditionally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
630824a238
gnu: julia-woodburymatrices: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-woodburymatrices)[arguments]<#:phases>:
Conditionally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
828012ed9f
gnu: julia-intervalsets: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-intervalsets)[arguments]<#:phases>:
Conditionally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:32 +02:00
29c0410086
gnu: julia-reversediff: Disable tests on i686-linux.
...
* gnu/packages/julia-xyz (julia-reversediff)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:31 +02:00
28d530ea44
gnu: julia-interpolations: Disable tests in i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-interpolations)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:31 +02:00
e3c15b0bfc
gnu: julia-arrayinterface: Disable tests for i686.
...
* gnu/packages/julia-xyz.scm (julia-arrayinterface)[arguments]<#:tests?>:
Conditionally disable tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:31 +02:00
7c8e9cbfa9
gnu: julia-mappedarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-mappedarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
dcd7c950c6
gnu: julia-blockarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-blockarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
557caa4e2c
gnu: julia-lazyarrays: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-lazyarrays)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
dbad333481
gnu: julia-configurations: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-configurations)[arguments]<#:phases>:
Conditionally replace the incorrect type in test suite.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:30 +02:00
a31a4517b6
gnu: julia-finitedifferences: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz (julia-finitedifferences)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
2a749f34e5
gnu: julia-benchmarktools: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-benchmarktools)[arguments]<#:phases>:
Conditionnally disable the failing tests.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
7fee8a46fb
gnu: julia-datastructures: Fix tests on i686-linux.
...
* gnu/packages/julia-xyz.scm (julia-datastructures)[arguments]<#:phases>:
Conditionnally disable the failing test.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:50:29 +02:00
9112bed608
gnu: libunwind-julia: Fix build on i686-linux.
...
* gnu/packages/julia.scm (libunwind)[origin]<patches>: Add patch.
* gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch: New file.
* gnu/local/mk (dist_patch_DATA): Register it.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-04 19:33:30 +02:00
f199427c1b
gnu: emacs-org-roam-bibtex: Update to 0.6.1.
...
* gnu/packages/emacs-xyz.scm (emacs-org-roam-bibtex): Update to 0.6.1.
2021-12-04 16:17:58 +01:00
cc491eab7e
gnu: plink-ng: Enable tests.
...
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
2021-12-04 16:00:08 +01:00
e28b8a9cea
gnu: plink-ng: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:35:28 +01:00
88bb81b515
gnu: plink: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace
reference to %build-inputs.
2021-12-04 15:31:31 +01:00
e920101141
gnu: plink: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from
build phase.
2021-12-04 15:31:08 +01:00
a4e7475edc
gnu: rsem: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
2021-12-04 15:27:39 +01:00
c45c909026
gnu: rsem: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:26:48 +01:00
5e0bcba57b
gnu: rsem: Remove references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp.
2021-12-04 15:26:01 +01:00
23975fe27a
gnu: rsem: Remove trailing #T from snippet.
...
* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T.
2021-12-04 15:25:26 +01:00
cfaf37d10b
gnu: prodigal: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-04 15:13:11 +01:00
09ae51f7b8
gnu: prank: Bind INPUTS in 'install phase.
...
* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install
phase to remove references to %build-inputs.
2021-12-04 15:11:28 +01:00
e128839a94
gnu: prank: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from
build phases.
2021-12-04 15:11:04 +01:00
da70132ee9
gnu: janet: Update to 1.19.0.
...
* gnu/packages/lisp.scm (janet): Update to 1.19.0.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04 13:51:49 +01:00
612fe425b4
gnu: tinmop: Update to 0.9.2.
...
* gnu/packages/web-browsers.scm (tinmop): Update to 0.9.2.
[inputs]: Move nano, openssl and xdg-utils to...
[native-inputs]: ... here. Add automake, autoconf and mandoc. Remove curl
and gnupg.
[arguments]: Add 'fix-configure.ac' phase.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-04 13:44:17 +01:00
18a85213ae
gnu: pigx-sars-cov2-ww: Update to 0.0.4.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4.
[inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
2021-12-04 12:42:51 +01:00
114eb987cb
gnu: mash: Replace references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp.
2021-12-04 00:32:01 +01:00
22d9097b5e
gnu: mash: Move htslib and capnproto to regular inputs.
...
* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and
capnproto from here...
[inputs]: ...to here.
2021-12-04 00:31:20 +01:00
a6b6084649
gnu: mash: Simplify snippet.
...
* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify.
2021-12-04 00:30:44 +01:00
31409a4af7
gnu: mafft: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from
build phase.
2021-12-04 00:22:27 +01:00
630671d2e8
gnu: mafft: Replace references to %build-inputs and %outputs.
...
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to
%outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs
phase by binding INPUTS.
2021-12-04 00:21:27 +01:00
5cb2920b8d
gnu: jellyfish: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp.
2021-12-04 00:19:08 +01:00
7c2ee27360
gnu: fastp: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp.
2021-12-04 00:16:10 +01:00
64aafe4bc5
gnu: java-picard: Replace reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (java-picard): Use a gexp.
2021-12-04 00:06:43 +01:00
a3b00a21c0
gnu: java-htsjdk: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp.
2021-12-04 00:03:54 +01:00
62e0641892
gnu: fxtract: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp.
2021-12-04 00:02:20 +01:00
4f03151ca4
gnu: delly: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-04 00:00:26 +01:00
3601fcbf65
gnu: libbigwig: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:57:24 +01:00
fd607a9efa
gnu: cd-hit: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to
%outputs with gexp.
2021-12-03 23:56:11 +01:00
c40852a227
gnu: bowtie1: Replace reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to
%outputs by using a gexp.
2021-12-03 23:54:10 +01:00
a47a90b900
gnu: bowtie: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to
%outputs with a gexp.
2021-12-03 23:52:43 +01:00
f5c38ee45f
gnu: bless: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to
%build-inputs with a gexp. Use the dynamic library of zlib while we're at it.
[inputs]: Remove zlib:static.
2021-12-03 23:51:16 +01:00
dd19c8da88
gnu: bless: Remove trailing #T from snippet and build phases.
...
* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all
trailing #Ts.
2021-12-03 23:48:46 +01:00
0e09065460
gnu: bedtools: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of
referencing %outputs.
2021-12-03 23:36:18 +01:00
a5663a7c8a
gnu: qtltools: Replace references to %build-inputs.
...
* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of
referencing %build-inputs.
2021-12-03 23:26:48 +01:00
ce9bfcddb5
gnu: imp: Update to 2.15.0.
...
* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0.
[arguments]: Disable one more test.
2021-12-03 22:29:52 +01:00
dcf857e486
gnu: Add r-fpeek.
...
* gnu/packages/cran.scm (r-fpeek): New variable.
2021-12-03 22:29:40 +01:00
15404ff19b
gnu: emacs: Load package descriptors from packages referenced by subdirs.el
...
* gnu/packages/aux-files/emacs/guix-emacs.el
(guix-emacs--non-core-load-path): New procedure.
(guix-emacs-autoload-packages): Use it here.
(guix-emacs-load-package-descriptors): New procedure.
* gnu/packages/emacs.scm (emacs)[install-site-start]: Install advice to run
‘guix-emacs-load-package-descriptors’.
2021-12-03 21:39:50 +01:00
4baeb72717
gnu: emacs: Make DocView PDF work out of the box.
...
* gnu/packages/emacs.scm (emacs)[patch-program-file-names]: Add patches for
the programs “gs”, “dvipdf”, “ps2pdf” and “pdftotext”.
[inputs]: Add ghostscript and poppler.
2021-12-03 21:39:49 +01:00
f725279cdd
gnu: emacs: Find real GVFS processes.
...
* gnu/packages/emacs.scm (emacs)[#:phases]<patch-program-file-names>: Expand
calls to “tramp-compat-process-running-p” so that Guix wrappers are also
matched.
2021-12-03 21:39:49 +01:00
269baba919
gnu: Add valeronoi.
...
* gnu/packages/engineering.scm (valeronoi): New variable.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:38:30 +01:00
19528e39bb
gnu: st: Install terminfo files.
...
* gnu/packages/suckless.scm (st)[native-inputs]: Add ncurses.
[make-flags](TERMINFO): New flag.
[phases](inhibit-terminfo-install): Remove phase.
Signed-off-by: Raghav Gururajan <rg@raghavgururajan.name>
2021-12-03 15:27:41 -05:00
170cb4c881
gnu: emacs-org: Preserve version information.
...
* gnu/packages/emacs-xyz.scm (emacs-org)[#:phases]: Prevent install phase from
deleting the version information.
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
2021-12-03 21:14:25 +01:00
85ed37c170
gnu: emacs-consult-notmuch: Update to 0.6.
...
* gnu/packages/emacs-xyz.scm (emacs-consult-notmuch): Update to 0.6.
2021-12-03 19:43:12 +01:00
6557f17000
gnu: emacs-helm: Update to 3.8.2.
...
* gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.2.
2021-12-03 19:41:27 +01:00
a7776d5ac0
gnu: emacs-vertico: Update to 0.17.
...
* gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.17.
2021-12-03 19:36:35 +01:00
b8d6e77476
gnu: python-ont-fast5-api: Update to 4.0.0.
...
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0.
[source]: Remove bundled plugin binaries.
[arguments]: Install plugin from inputs.
[inputs]: Add vbz-compression.
[propagated-inputs]: Remove python-six; add python-packaging.
2021-12-03 14:55:38 +01:00
d0aa14a43d
gnu: Add vbz-compression.
...
* gnu/packages/bioinformatics.scm (vbz-compression): New variable.
2021-12-03 14:55:38 +01:00
3354e41c1e
system: vm: Remove the vga argument.
...
* gnu/system/vm.scm (common-qemu-options): Remove the "-vga std" argument that
is the default since QEMU 2.2.
Suggested-by: Attila Lendvai <attila@lendvai.name>
2021-12-03 14:25:57 +01:00
b42bfbdfe5
guix system vm: Add --no-graphic CLI argument.
...
It configures QEMU to use the tty it was started in for IO (as opposed to
opening a separate graphical window). This enables copy-pasting and
scrollback. Exit QEMU with C-a x.
* gnu/system/vm.scm (system-qemu-image/shared-store-script): Also add the
'-nographic' QEMU argument when called with #:graphic? #false.
* guix/scripts/system.scm (system-derivation-for-action): Propagate
the #:graphic? keyword arg.
(perform-action): Add and propagate the #:graphic? keyword arg.
(show-help): Add --no-graphic CLI arg.
(%options): Process the new --no-graphic CLI arg.
(process-action): Feed in the CLI arg through the #:graphic? keyword arg.
* doc/guix.texi (Invoking guix system): Add example to combine guix system and
invoking the vm start script into one command. Split the description of the
various options into separate paragraphs. Add a paragraph to describe
--no-graphic.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03 14:18:32 +01:00
5a18cf3604
gnu: cl-coalton: Update to 0.0.1-2.012f6c8.
...
* gnu/packages/lisp-xyz.scm (sbcl-coalton): Update to 0.0.1-2.012f6c8.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03 14:08:14 +01:00
6e0c4a28b9
gnu: cl-float-features: Update to 1.0.0-2.c1f86ae.
...
* gnu/packages/lisp-xyz.scm (sbcl-float-features): Update to 1.0.0-2.c1f86ae.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-12-03 13:59:46 +01:00
6d4f260166
gnu: bamutils: Update to 1.0.14.
...
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.14.
[arguments]: Patch DATE for reproducibility; prepare sources of libstatgen.
[native-inputs]: Add sources of libstatgen.
2021-12-03 13:56:02 +01:00
673cc29908
gnu: bamutils: Remove reference to %outputs.
...
* gnu/packages/bioinformatics.scm (bamutils)[arguments]: Use gexp.
2021-12-03 13:56:01 +01:00
361e0d9f27
gnu: bamm: Remove reference to %build-inputs.
...
* gnu/packages/bioinformatics.scm (bamm)[arguments]: Use gexp instead of
%build-inputs.
2021-12-03 13:56:01 +01:00
4f536c4607
gnu: python2-openpyxl: Explicitly build with Python 2.
...
* gnu/packages/python-xyz.scm (python2-openpyxl)[arguments]: Add value
for #:python field.
2021-12-03 13:56:01 +01:00
7fb5bfc54f
gnu: python-plastid: Update to 0.5.1.
...
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.5.1.
2021-12-03 13:56:01 +01:00
b7aaf6c418
gnu: ivar: Disable parallel tests.
...
* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
2021-12-03 13:48:41 +01:00
aa2d5ca02e
gnu: Remove python2-biom-format.
...
There are no users of this variant, and the current version of biom-format
does not support Python 2.
* gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable.
(python-biom-format)[properties]: Remove field.
2021-12-03 13:31:32 +01:00
8fa7de386c
gnu: r-flowclust: Add gsl.
...
* gnu/packages/bioconductor.scm (r-flowclust)[inputs]: Remove accidentally
committed comment character.
2021-12-03 13:31:32 +01:00
3e9dc2754e
gnu: icecat: Remove vestigial icecat-78-makeicecat.patch.
...
This is a followup to commit a63231003e
2021-12-03 04:45:15 -05:00
c0d9ba22d0
gnu: cuirass: Update to 1.1.0-6.df8837c.
...
* gnu/packages/ci.scm (cuirass): Update to 1.1.0-6.df8837c.
2021-12-03 10:41:37 +01:00
fcf7e6513c
gnu: python-pandocfilters: Update to 1.5.0.
...
* gnu/packages/textutils.scm (python-pandocfilters): Update to 1.5.0.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-03 10:41:37 +01:00
Ricardo Wurmus
Marius Bakke
Nicolas Goaziou
Sharlatan Hellseher
dissent
jgart
Efraim Flashner
Artyom V. Poptsov
Vivien Kraus
Ryan Desfosses
Ludovic Courtès
Julien Lepiller
zimoun
cage
Liliana Marie Prikler
phodina
Morgan Smith
Mathieu Othacehe
Attila Lendvai
Charles
Mark H Weaver