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python2-biopython has been removed from Guix upstream.
* gn/packages/bioinformatics.scm (python2-biopython): New variable.
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* gn/packages/bioinformatics.scm: Import (gnu packages ocaml) required
by dependencies of pplacer.
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pplacer and pplacer-scripts have been removed from Guix upstream.
* gn/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
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python-pytest-runner-2 has been removed from Guix upstream.
* gn/packages/bioinformatics.scm (python-pytest-runner-2): New
variable.
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- Genenetwork3 depends on diffutils
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Add a package definition for the GeneNetwork Quality Control
application.
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*
gn/services/databases.scm (<virtuoso-configuration>)[maximum-dirty-buffers]:
New field.
(virtuoso-shepherd-service): Serialize maximum-dirty-buffers field.
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gn/services/databases.scm (<virtuoso-configuration>)[number-of-buffers]:
New field.
(virtuoso-shepherd-service): Serialize number-of-buffers field.
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* gn/packages/riscv.scm (cva6)[arguments]: Set #:make-flags instead of
overriding the build phase.
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* gn/packages/riscv.scm (cva6)[source]: Use upstream openhwgroup
source instead of the cornell-brg fork.
[arguments]: Add fix-stdout phase. Pass RISV=0 to make in build phase.
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* gn/packages/riscv.scm (cva6)[arguments]: In the custom install
phase, install executable as ariane instead of Variane_testharness.
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* gn/packages/riscv.scm: Import (gn packages fpga), (gnu packages
virtualization), (guix build utils), (guix build-system gnu), (guix
gexp) and (guix licenses).
(cva6): New variable.
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* gn/packages/fpga.scm: New file.
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* gn/packages/gemini.scm (skribilo-with-gemtext-reader): Rename to
skribilo-latest and switch to the latest commit on the master branch.
(tissue)[propagated-inputs]: Replace skribilo-with-gemtext-reader with
skribilo-latest.
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* gn/packages/gemini.scm (tissue)[arguments]: In the custom
patch-source-shebangs phase, set the absolute path to guile, not git,
in the shebang.
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* gn/packages/gemini.scm (tissue)[arguments]: Replace the
patch-source-shebangs phase with a custom one.
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* gn/packages/genenetwork.scm: Update commit and hash.
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* gn/packages/gemini.scm (tissue): Update to 0.1.0-0.85811ab.
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GN2 on the testing branch relies on features in GN3 that are not
present in commit 16367dab9248d3aa2660e0b5cafdce25e8f7067c of
GN3. This commit thus updates the dependency to get the latest version
of GN3 that is building successfully.
Signed-off-by: BonfaceKilz <me@bonfacemunyoki.com>
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python-rpy2@3.4.5 has been upstreamed.
* gn/packages/python.scm (python-rpy2-next): Delete variable.
* gn/packages/genenetwork.scm (genenetwork2)[propagated-inputs]:
Replace python-rpy2-next with python-rpy2.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn/packages/statistics.scm (r-ctl): Update to 1.0.0-7.
[source]: Use cran-uri.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn/packages/static.scm (smithwaterman-static): New variable.
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change unlicense
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* gn/packages/gemini.scm (tissue)[arguments]: In the custom configure
phase, substitute absolute path to git in tissue/git.scm, but not in
tissue/web.scm.
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* gn/packages/gemini.scm (tissue): Update to 0.1.0-0.25104d4.
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* gn/packages/gemini.scm (skribilo-with-gemtext-reader): Update to
0.9.5-0.8d4f4c8.
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upstreamed: https://issues.guix.gnu.org/54712
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todo:
fix tests: https://github.com/NixOS/nixpkgs/blob/nixos-21.11/pkgs/development/python-modules/supervisor/default.nix#L16
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