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2023-12-29Ruby lmdb builds for ruby 2.7. We are not going to use it thoughpjotrp
2023-12-05gn-auth: add flask-cors dependency.Frederick Muriuki Muriithi
2023-12-05gn-auth: Remove bcrypt dependencyFrederick Muriuki Muriithi
2023-12-01roll-back on lizardfs because fuse3 issuespjotrp
2023-11-16Updated lizardfs to latest version on git.pjotrp
* gn/packages/file-systems.scm (lizardfs)[arguments]: updated and disabled tests in CMake
2023-11-16Added note on move to https://git.genenetwork.org/guix-bioinformatics/pjotrp
2023-11-13gn: javascript: Add javascript-aceAlexander_Kabui
* gn/packages/javascript.scm (javascript-ace): New package. Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-10gn: javascript: Add javascript-marked-highlight.Alexander_Kabui
* gn/packages/javascript.scm (javascript-marked-highlight): New package. Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-10gn: javascript: Add javascript-marked.Alexander_Kabui
* gn/packages/javascript.scm (javascript-marked): New package. Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-08gn: lizardfs: Fix building.Efraim Flashner
* gn/packages/file-systems.scm (lizardfs)[source]: Add patch. [arguments]: Remove trailing #t from phases. [inputs]: Remove labels. Use fuse-2. * lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch: New file.
2023-11-03gn: javascript: Copy the right htmx.min.js from the source.Munyoki Kilyungi
* gn/packages/javascript.scm (javascript-htmx): Copy "/dist/htmx.min.js" to the targetdir. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Update dependencies: genenetwork3 and gn-authFrederick Muriuki Muriithi
* genenetwork3: Remove `yoyo-migrations` as a dependency * gn-auth: Use the upstream `yoyo-migrations` * Remove temporary local definition for yoyo-migrations.
2023-10-26gn: htmx: Replace minify with trivial build system.Munyoki Kilyungi
Esbuild system has no support for ES5 and will lead to a build failure with the following output: `dist/htmx.js:1979:20: error: Transforming let to the configured target environment ("es5") is not supported yet` Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Upgrade guix channel to 330b94e.Arun Isaac
2023-10-19Remove python-arvados-python-client.Arun Isaac
The package is broken, some of its inputs have been removed from upstream Guix, and we no longer need this package. Restore it later if necessary. * gn/packages/python.scm (python-arvados-python-client): Delete variable.
2023-10-19Remove bh20-seq-resource.Arun Isaac
The package is broken, some of its inputs have been removed from upstream Guix, and we no longer need this package. * gn/packages/bioinformatics.scm (bh20-seq-resource): Delete variable. * gn/services/bh20-seq-resource-container.scm: Delete file.
2023-10-06genenetwork3: Add python-pyld to propagated-inputs.Munyoki Kilyungi
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add python-ld. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-04gn: javascript: Replace htmx.min.js with htmx.js.Munyoki Kilyungi
* gn/packages/javascript.scm (javascript-htmx) [arguments]: Replace "dist/htmx.min.js" with "dist/htmx.js" since we already are using the minify-build-system. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-27gn-auth: Fix missing importFrederick Muriuki Muriithi
2023-09-27gn-auth: List packages to installFrederick Muriuki Muriithi
List all packages to install to hopefully fix failure in `sanity-check` phase.
2023-09-27gn-auth: Use newer setup.pyFrederick Muriuki Muriithi
Use updated setup.py to try and fix issues with the `sanity-check` phase.
2023-09-27gn-auth: Use upstream python-mypyFrederick Muriuki Muriithi
2023-09-27gn-auth: Update commit and hashFrederick Muriuki Muriithi
* Update the commit hash and the hash of the files after updating the guix-bioinformatics channel configurations for the gn-auth channel.
2023-09-27gn-auth: Update commit and hash.Frederick Muriuki Muriithi
2023-09-26pggb: Add missing inputsEfraim Flashner
2023-09-26pggb: wrap with more packagesEfraim Flashner
2023-09-26gsl: Provide glibc-hwcaps version.Efraim Flashner
2023-09-26vg: Update package definitionEfraim Flashner
2023-09-26seqwish: Provide glibc-hwcaps versionEfraim Flashner
2023-09-26seqwish: Build and link against shared library.Efraim Flashner
2023-09-25seqwish: Make package tunable.Efraim Flashner
2023-09-25vg: Link with some shared libraries.Efraim Flashner
2023-09-25Delete python-mypy-0.981.Munyoki Kilyungi
* gn/packages/python.scm (python-mypy-0.981): Delete it. * gn/packages/genenetwork.scm (genenetwork3)[native-inputs]: Replace python-mypy-0.981 with upstream's python-mypy. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-24pggb: Fix typo.Efraim Flashner
2023-09-24pggb: Provide version with glibc-hwcaps.Efraim Flashner
2023-09-24Provide copy of sdsl-lite with glibc-hwcapsEfraim Flashner
2023-09-24smoothxg: Link with odgiEfraim Flashner
2023-09-24smoothxg: Link with sdsl-liteEfraim Flashner
2023-09-24seqwish: Link with sdsl-libEfraim Flashner
2023-09-24pggb: Remove python-pycairoEfraim Flashner
2023-09-24rtg-tools: Use a smaller java implementationEfraim Flashner
2023-09-24pggb: Add htslib for tabix dependency.Efraim Flashner
2023-09-22Add pggb.Efraim Flashner
2023-09-22vg: Prepare for using a shared library.Efraim Flashner
2023-09-22vg: Update to 1.50.0.Efraim Flashner
2023-09-21rtg: Update package definition.Efraim Flashner
2023-09-21mummer: Update to 4.0.0rc1.Efraim Flashner
2023-09-21odgi: Add variant with glibc-hwcaps.Efraim Flashner
2023-09-21wfmash: Fix typos.Efraim Flashner
2023-09-21odgi: Update to 0.8.3.Efraim Flashner
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