guix-bioinformatics - Bioinformatics packages for GNU Guix

Age	Commit message (Collapse)	Author
2022-01-01	genenetwork3: updated and disabled tests	Pjotr Prins

2022-01-01	genenetwork2: put a hack in to fix failing build. Please amend	Pjotr Prins

2021-12-29	gnu: Add python2-bx-python.	Arun Isaac
	python2-bx-python has been removed from upstream Guix. * gn/packages/bioinformatics.scm (python2-bx-python): New variable.
2021-12-29	Reference 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 @@.
2021-12-29	Fix typo in import of (gnu packages textutils).	Arun Isaac
	* gn/packages/genenetwork.scm: Import (gnu packages textutils), not (gn packages textutils).
2021-12-29	gn: 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.
2021-12-21	gn/packages/genenetwork.scm: Use csvdiff from textutils.	BonfaceKilz
	* gn/packages/genenetwork.scm (genenetwork2): Use updated version of csvdiff from textutils.
2021-12-12	gn: gitea: don't patch shebangs of repo actions	Efraim Flashner

2021-12-10	gn: ccwl: Remove package.	Arun Isaac
	ccwl has been upstreamed. * gn/packages/ccwl.scm: Delete file.
2021-12-09	gn: 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.
2021-12-09	gn: 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.
2021-12-07	remove pudb	jgart
	https://issues.guix.gnu.org/52177
2021-12-06	gn: Add mutation-simulator	Efraim Flashner

2021-12-03	add pudb	jgart

2021-12-01	Remove julia packages: softglobalscope, jive, and millboard.	jgart
	I sent them to upstream: https://issues.guix.gnu.org/52213 https://issues.guix.gnu.org/52211
2021-11-30	gn: services: databases: Export virtuoso-service-type.	Arun Isaac
	* gn/services/databases.scm: Export virtuoso-service-type.
2021-11-30	gnu: services: Add virtuoso service.	Arun Isaac
	* gn/services/databases.scm: New file.
2021-11-26	gemma-wrapper: bug fix	pjotrp

2021-11-25	Updated gemma-wrapper	pjotrp

2021-11-19	gnu: Add julia-jive.	jgart
	* gn/packages/julia.scm (julia-jive): New variable.
2021-11-19	gnu: Add julia-millboard.	jgart
	* gn/packages/julia.scm (julia-millboard): New variable.
2021-11-19	gnu: Add julia-softglobalscope.	jgart
	* gn/packages/julia.scm (julia-softglobalscope): New variable.
2021-11-19	gnu: Add python-requirements-parser.	jgart
	* gn/packages/python.scm (python-requirements-parser): New variable.
2021-11-17	gn: genenetwork: Add javascript-xterm , javascript-xterm-style, ↵	Alexander Kabui
	javascript-xterm-addon-fit to genenetwork2 * gn/packages/genenetwork.scm(genenetwork2) [propagated-inputs]: Add javascript-xterm , javascript-xterm-style and javascript-xterm-addon-fit
2021-11-17	gn: javascript: Add javascript-xterm-addon-fit	Alexander Kabui
	* gn/packages/javascript.scm: (javascript-xterm-addon-fit): New package
2021-11-16	gn: metaeuk: enable tests.	Efraim Flashner

2021-11-16	gn: Adjust to changes in julia-build-system	Efraim Flashner

2021-11-16	gn: python-sparqlwrapper: Remove package.	Arun Isaac
	python-sparqlwrapper has been upstreamed. * gn/packages/python.scm (python-sparqlwrapper): Delete variable.
2021-11-15	gn: Add sepp, busco	Efraim Flashner

2021-11-14	gn: Add augustus	Efraim Flashner

2021-11-14	gn: add metaeuk	Efraim Flashner

2021-11-14	gn: bh2-seq-resource: Update source uri, homepage	Efraim Flashner

2021-11-10	Remove python-flask-socketio.	Arun Isaac
	python-flask-socketio has been upstreamed. * gn/packages/python.scm (python-flask-socketio): Delete variable.
2021-11-08	gn: Remove upstreamed packages.	Arun Isaac
	* gn/packages/python.scm (python-webcolors): Delete variable. * gn/packages/messaging.scm: Delete file.
2021-11-05	gn: genenetwork: Remove unused package inputs	BonfaceKilz

2021-11-05	gn: genenetwork: Delete dead comments	BonfaceKilz

2021-11-05	gemma-wrapper: rolling back on parallel	Pjotr Prins

2021-11-04	gn: Update genenetwork3 to 0.0.1-guix-9e0fa5f	BonfaceKilz

2021-11-04	gnu: Add weechat-wee-slack.	Arun Isaac
	* gn/packages/messaging.scm (weechat-wee-slack): New variable.
2021-11-04	gnu: Add weechat-matrix.	Arun Isaac
	* gn/packages/messaging.scm: New file.
2021-11-04	gnu: Add python-webcolors.	Arun Isaac
	* gn/packages/python.scm (python-webcolors): New variable.
2021-11-01	gn: Add python-pingouin	BonfaceKilz
	* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add python-pingouin
2021-10-29	gn: fix texinfo markup	Efraim Flashner

2021-10-27	gn: python-htmlgen: Download using git-fetch.	Efraim Flashner

2021-10-27	gn: genenetwork: Add python-deprecated	BonfaceKilz
	Only used when deemed necessary.
2021-10-24	gn: julia packaging	Efraim Flashner

2021-10-24	gn: julia packages upstreamed	Efraim Flashner

2021-10-20	gn: readying julia packages for upstreaming.	Efraim Flashner

2021-10-20	gn: package upstreamed	Efraim Flashner

2021-10-18	gn: move kaleido to its own branch.	Efraim Flashner
	The use of guix inferiors was making using the guix-bioinformatics repository incredibly slow.