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2022-06-07gn: python2-biopython: Fix building package.Efraim Flashner
2022-06-07gn: Fix building python2-rpy2.Efraim Flashner
2022-06-07gn: Hide inputs which have been dropped by Guix.Efraim Flashner
2022-06-07gn: Add missing module importsEfraim Flashner
2022-06-07gn: cleanup yaj importsEfraim Flashner
2022-06-01gn: Add python2-biopython.Arun Isaac
python2-biopython has been removed from Guix upstream. * gn/packages/bioinformatics.scm (python2-biopython): New variable.
2022-06-01gn: bioinformatics: Import (gnu packages ocaml).Arun Isaac
* gn/packages/bioinformatics.scm: Import (gnu packages ocaml) required by dependencies of pplacer.
2022-06-01gnu: Add pplacer.Arun Isaac
pplacer and pplacer-scripts have been removed from Guix upstream. * gn/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
2022-06-01gnu: Add python-pytest-runner-2.Arun Isaac
python-pytest-runner-2 has been removed from Guix upstream. * gn/packages/bioinformatics.scm (python-pytest-runner-2): New variable.
2022-06-01gn: Adjust vg for other architecturesEfraim Flashner
2022-06-01ruby-cbor upstreamedEfraim Flashner
2022-05-24New dependency: (genenetwork3: diffutils)Frederick Muriuki Muriithi
- Genenetwork3 depends on diffutils
2022-05-11genenetwork-qc: Update the releaseFrederick Muriuki Muriithi
2022-05-09Add definition for genenetwork-qcFrederick Muriuki Muriithi
Add a package definition for the GeneNetwork Quality Control application.
2022-05-05services: databases: Add virtuoso maximum dirty buffers configuration.Arun Isaac
* gn/services/databases.scm (<virtuoso-configuration>)[maximum-dirty-buffers]: New field. (virtuoso-shepherd-service): Serialize maximum-dirty-buffers field.
2022-05-05services: databases: Add virtuoso number of buffers configuration.Arun Isaac
* gn/services/databases.scm (<virtuoso-configuration>)[number-of-buffers]: New field. (virtuoso-shepherd-service): Serialize number-of-buffers field.
2022-05-03gn: cva6: Set #:make-flags instead of overriding the build phase.Arun Isaac
* gn/packages/riscv.scm (cva6)[arguments]: Set #:make-flags instead of overriding the build phase.
2022-05-03gn: cva6: Switch to upstream source instead of fork.Arun Isaac
* 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.
2022-05-02gn: cva6: Install executable as ariane.Arun Isaac
* gn/packages/riscv.scm (cva6)[arguments]: In the custom install phase, install executable as ariane instead of Variane_testharness.
2022-05-02gn: Add cva6.Arun Isaac
* 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.
2022-05-02gn: Add verilator-4.110.Arun Isaac
* gn/packages/fpga.scm: New file.
2022-04-20Remove upstreamed packagesEfraim Flashner
2022-04-20gn: Add wfa2-lib-static.Efraim Flashner
2022-04-20gn: wfa2-lib: Install headers.Efraim Flashner
2022-04-20gn: skribilo-with-gemtext-reader: Update to 0.9.5-1.621eb19.Arun Isaac
* 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.
2022-04-19gn: Add wfa2-lib.Efraim Flashner
2022-04-15gn: tissue: Set absolute path to guile, not git, in shebang.Arun Isaac
* gn/packages/gemini.scm (tissue)[arguments]: In the custom patch-source-shebangs phase, set the absolute path to guile, not git, in the shebang.
2022-04-15gn: tissue: Set absolute path to guile in shebang.Arun Isaac
* gn/packages/gemini.scm (tissue)[arguments]: Replace the patch-source-shebangs phase with a custom one.
2022-04-14notebooks: add cl-nbjgart
2022-04-14notebooks: move nb-uploadjgart
2022-04-14nb-upload: update to b285302jgart
2022-04-14Update genetwork3 to 39afc68BonfaceKilz
* gn/packages/genenetwork.scm: Update commit and hash.
2022-04-14gn: tissue: Update to 0.1.0-0.85811ab.Arun Isaac
* gn/packages/gemini.scm (tissue): Update to 0.1.0-0.85811ab.
2022-04-13Update GN3 to latest commitFrederick Muriuki Muriithi
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>
2022-04-12gn: python-rpy2-next: Remove package.Alexander
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>
2022-04-12gn: r-ctl: Update to 1.0.0-7.Alexander
* gn/packages/statistics.scm (r-ctl): Update to 1.0.0-7. [source]: Use cran-uri. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-04-10gn: vg: Update to 1.39.0.Efraim Flashner
2022-04-08gn: Add smithwaterman-static.Arun Isaac
* gn/packages/static.scm (smithwaterman-static): New variable.
2022-04-07qc: update to a0d8c80jgart
change unlicense
2022-04-07nb-upload: update to 3e8fe60jgart
2022-04-07binderlite: add nb-uploadjgart
2022-04-06gn: tissue: Substitute git path in tissue/git.scm.Arun Isaac
* 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.
2022-04-06quality-control: add WIP sbcl-qc-uploads packagejgart
2022-04-06move sbcl-qc to quality-control modulejgart
2022-04-06gn: tissue: Update to 0.1.0-0.25104d4.Arun Isaac
* gn/packages/gemini.scm (tissue): Update to 0.1.0-0.25104d4.
2022-04-06gn: skribilo-with-gemtext-reader: Update to 0.9.5-0.8d4f4c8.Arun Isaac
* gn/packages/gemini.scm (skribilo-with-gemtext-reader): Update to 0.9.5-0.8d4f4c8.
2022-04-05remove python-dotenv-for-binderlitejgart
upstreamed: https://issues.guix.gnu.org/54712
2022-04-04add python-dotenv-for-binderlitejgart
2022-04-04gn: packages: python: add python-supervisorjgart
todo: fix tests: https://github.com/NixOS/nixpkgs/blob/nixos-21.11/pkgs/development/python-modules/supervisor/default.nix#L16
2022-04-04gn: binderlite: add python-jgart-giturlparsejgart