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2022-01-26gn: packages: quality-control: remove utf-8-lineseparatorjgart
* upstreamed to GNU Guix
2022-01-26gn: genenetwork: Disable tests on python-seaborn.Arun Isaac
* gn/packages/genenetwork.scm (python-seaborn-without-tests, python-pingouin-with-working-python-seaborn): New variables. (genenetwork3)[propagated-inputs]: Replace python-pingouin with python-pingouin-with-working-python-seaborn.
2022-01-26gn: packages: lisp: Add cl-scribble.jgart
2022-01-26gn: packages: lisp: Add cl-meta.jgart
2022-01-26gn: packages: lisp: Add cl-fare-memoization.jgart
2022-01-26gn: packages: lisp: Add cl-lorem-ipsum.jgart
2022-01-26gn: packages: lisp: Add sbcl-fwoar-lisputils.jgart
2022-01-26gn: packages: lisp: Add cl-2am.jgart
2022-01-26gn: packages: lisp: Add cl-defstar.jgart
2022-01-26gn: packages: Add cl-snakes.jgart
2022-01-26gn: packages: lisp: Add sbcl-rollbar.jgart
2022-01-26gn: packages: utf-8-lineseparator: Don't use tag name in version field.jgart
2022-01-25gn: Fix failing python-twint build.BonfaceKilz
* gn/packages/twint.scm (python-aiohttp-3.7.2): Delete it. (python-aiohttp-socks-0.5.5): Delete it. (python-yarl-1.6.2): Delete it. (python-twint) [propagated-inputs]: Replace python-aiohttp-socks-0.5.5 with python-aiohttp-socks and python-yarl-1.6.2 with python-yarl.
2022-01-24gn: quality-control: add libcsvjgart
2022-01-24gn: utf-8-lineseparator: Update to cj7.jgart
2022-01-23gn: Add verkko.Efraim Flashner
2022-01-23gn: graphaligner: Fix building and update to 1.0.14Efraim Flashner
2022-01-22gn: gemma-wrapper: added coreutils and note on testingpjotrp
2022-01-22gn: gemma-wrapper: updated to 0.99.6pjotrp
2022-01-22gn: gemma-wrapper: updated to 0.99.6pjotrp
2022-01-13gn: quality-control: Add utf-8-lineseparator.jgart
* gn/packages/quality-control.scm: New file.
2022-01-09gn: Remove upstreamed node packagesEfraim Flashner
2022-01-09gn: Unconditionally use current rust package.Efraim Flashner
2022-01-09gn: check for new releases of giteaEfraim Flashner
2022-01-06gn: genenetwork: Add diffutilsBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add diffutils.
2022-01-05Revert "gn: genenetwork: Add pudb"BonfaceKilz
This reverts commit f7e876d53832cf1d5d4b19118266e910e6100ea9. Add an extra dependency by running something like: ``` guix shell -L /home/bonface/projects/guix-bioinformatics \ -L /home/bonface/projects/guix-past/modules -C \ -D pudb -f guix.scm ```
2022-01-05gn: genenetwork: Add pudbBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add pudb for trouble-shooting purposes.
2022-01-01genenetwork3: updated and disabled testsPjotr Prins
2022-01-01genenetwork2: put a hack in to fix failing build. Please amendPjotr Prins
2021-12-29gnu: Add python2-bx-python.Arun Isaac
python2-bx-python has been removed from upstream Guix. * gn/packages/bioinformatics.scm (python2-bx-python): New variable.
2021-12-29Reference non-public rust packages using @@.Arun Isaac
rust-1.47 and rust-1.49 are no longer exported from (gnu packages rust). * gn/packages/bioinformatics.scm (gfaffix): Reference rust-1.49 using @@. * gn/packages/crates-io.scm (rust-handlegraph-0.7): Reference rust-1.47 using @@.
2021-12-29Fix typo in import of (gnu packages textutils).Arun Isaac
* gn/packages/genenetwork.scm: Import (gnu packages textutils), not (gn packages textutils).
2021-12-29gn: ldc: Use ldc-bootstrap-0.17.Arun Isaac
Upstream has renamed ldc-bootstrap to ldc-bootstrap-0.17. * gn/packages/dlang.scm (ldc): Inherit from ldc-bootstrap-0.17 instead of ldc-bootstrap. [native-inputs]: Replace ldc-bootstrap with ldc-bootstrap-0.17.
2021-12-21gn/packages/genenetwork.scm: Use csvdiff from textutils.BonfaceKilz
* gn/packages/genenetwork.scm (genenetwork2): Use updated version of csvdiff from textutils.
2021-12-12gn: gitea: don't patch shebangs of repo actionsEfraim Flashner
2021-12-10gn: ccwl: Remove package.Arun Isaac
ccwl has been upstreamed. * gn/packages/ccwl.scm: Delete file.
2021-12-09gn: genenetwork: Define version using git-version.Arun Isaac
Also, semantic versioning starts from 0.1.0, not 0.0.1. * gn/packages/genenetwork.scm (genenetwork3)[version]: Use git-version.
2021-12-09gn: genenetwork: Reorganize inputs.Arun Isaac
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Remove python-sqlalchemy-stubs. Add python-sparqlwrapper and rust-qtlreaper. Sort all inputs.
2021-12-07remove pudbjgart
https://issues.guix.gnu.org/52177
2021-12-06gn: Add mutation-simulatorEfraim Flashner
2021-12-03add pudbjgart
2021-12-01Remove julia packages: softglobalscope, jive, and millboard.jgart
I sent them to upstream: https://issues.guix.gnu.org/52213 https://issues.guix.gnu.org/52211
2021-11-30gn: services: databases: Export virtuoso-service-type.Arun Isaac
* gn/services/databases.scm: Export virtuoso-service-type.
2021-11-30gnu: services: Add virtuoso service.Arun Isaac
* gn/services/databases.scm: New file.
2021-11-26gemma-wrapper: bug fixpjotrp
2021-11-25Updated gemma-wrapperpjotrp
2021-11-19gnu: Add julia-jive.jgart
* gn/packages/julia.scm (julia-jive): New variable.
2021-11-19gnu: Add julia-millboard.jgart
* gn/packages/julia.scm (julia-millboard): New variable.
2021-11-19gnu: Add julia-softglobalscope.jgart
* gn/packages/julia.scm (julia-softglobalscope): New variable.
2021-11-19gnu: Add python-requirements-parser.jgart
* gn/packages/python.scm (python-requirements-parser): New variable.
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