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2023-09-19remove unneeded module importEfraim Flashner
2023-09-19Update pluto serverEfraim Flashner
2023-09-19update julia-visualsEfraim Flashner
2023-09-19Remove `rust-clap-4`...There is a `rust-clap-4` package upstream. Frederick Muriuki Muriithi
2023-09-06gn: gn-auth: Update yoyo and mypy...Update yoyo and mypy to allow the use of Python-3.10 Frederick Muriuki Muriithi
2023-09-05gn: genenetwork: Update mypy and yoyo...* gn/packages/genenetwork.scm: Import (guix packages). (genenetwork3): Use yoyo-migrations v8.2.0 and python-mypy v0.981. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05gn: python: Add python-mypy-0.981...* gn/packages/python.scm (python-mypy-0.981): New package. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05gn: python: Add yoyo-migrations-8.2.0...* gn/packages/python.scm: Import (gnu packages databases) and (guix hg-download). (yoyo-migrations-8.2.0): New package. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Adjust how native/propagated inputs are defined for GN3...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Update pinned guix version....guix-channel: Use guix at commit 8d70ff3a49f7cdf0eab93b3a1c54ec2f016afc4a. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Revert "Pin python to python@3.8.5"...This reverts commit aaa6e53e7b623105d05e67e95186aba5b4671010. Munyoki Kilyungi
2023-09-04Remove guix-forge channel...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Specify default branch for forge channel...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Add trailing slash to forge url...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Fix channel introduction...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Fix channel introduction...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Fix channel introduction in guix-forge...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Add guix-forge as an extra channel dependency...* .guix-channel: Add guix-forge. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-04Pin python to python@3.8.5...* gn/packages/genenetwork.scm: (genenetwork3, genenetwork2): Using python@3.8.5 Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-31Move gn-auth to (gn packages genenetwork).Arun Isaac
2023-08-31Downgrade guix to a4e9842.Arun Isaac
2023-08-31Revert "Pin guix-bioinformatics to commit with Python-3.9"...This reverts commit 0d743eb249bbdb67009d23ee53b2ee0ae881f725. Arun Isaac
2023-08-31Pin guix-bioinformatics to commit with Python-3.9...A number of GeneNetwork services/applications will not run with Python-3.10. This commit pins guix-bioinformatics to a specific commit to allow use of the older Python-3.10 before we are able to update everything needed to get them running on Python-3.10 Frederick Muriuki Muriithi
2023-08-30Replace `(...) with (list ...): Fixes "undefined gexp" failure....Replace the backquoted expression in the (arguments ...) section of the package definition to fix the error where the build could not find the variable gexp Frederick Muriuki Muriithi
2023-08-30Add missing `(guix gexp) module. Update package commit.Frederick Muriuki Muriithi
2023-08-25gn-auth: New packageFrederick Muriuki Muriithi
2023-08-12Added note on move to https://git.genenetwork.org/guix-bioinformatics/pjotrp
2023-07-06Remove tissue....tissue is now in upstream Guix. * gn/packages/gemini.scm: Delete file. Arun Isaac
2023-07-05gn: genenetwork3: Update to 0.1.0-3.f52247c....* gn/packages/genenetwork.scm (genenetwork3): Update to 0.1.0-3.f52247c. Arun Isaac
2023-07-05Run genenetwork3 tests using pytest....* gn/packages/genenetwork.scm (genenetwork3)[arguments]: Replace check phase to use pytest. Arun Isaac
2023-07-04Remove deprecated #:asd-files argument....* gn/packages/lisp.scm (sbcl-defstar, sbcl-2am, sbcl-fare-memoization, sbcl-meta, sbcl-scribble), gn/packages/notebooks.scm (sbcl-nb), gn/packages/quality-control.scm (sbcl-qc): Remove #:asd-files argument. Arun Isaac
2023-06-29Upgrade guix channel to d4e9ad2.Arun Isaac
2023-06-29 gn: gemma: Fix build using latest gccpjotrp
2023-06-26Fix DirsAllowed parameter...* gn/services/databases.scm (virtuoso-shepherd-service): Remove square brackets that sorround the DirsAllowed parameter. Munyoki Kilyungi
2023-06-26Merge branch 'add-virtuoso-allowed-dirs' into 'master'...Add dirs-allowed to virtuoso configs See merge request genenetwork/guix-bioinformatics!24BonfaceKilz
2023-06-23Fix indentation....* .guix-channel: Fix indentation. Arun Isaac
2023-06-22Fix "channel dependency has an invalid introduction field" error...* .guix-channel: Update how channel dependencies are defined to match: https://guix.gnu.org/manual/en/html_node/Declaring-Channel-Dependencies.html Munyoki Kilyungi
2023-06-20Add dirs-allowed to virtuoso configsMunyoki Kilyungi
2023-06-18Remove unused twint from GN2pjotrp
2023-06-15Uncommitted genome browser changesEfraim Flashner
2023-06-15Update pluto service and dependant julia packagesEfraim Flashner
2023-06-14gn: genecup: Use correct python-h5py....* gn/packages/python.scm (python-h5py-2): New variable. * gn/packages/machine-learning.scm (tensorflow-native): Remove comments. * gn/packages/ratspub.scm (use-corrected-inputs): New procedure. (genecup-with-tensorflow-native, genecup-latest-with-tensorflow-native): Use use-corrected-inputs. Efraim Flashner
2023-04-19gn: Update GN2 to 3.11-2.bfe557dcFrederick Muriuki Muriithi
2023-04-19gn: Update GN3 to 0.1.0-2.85610fc9Frederick Muriuki Muriithi
2023-04-10vg: Use curl instead of curl-minimal....curl-minimal has been removed from upstream Guix. * gn/packages/bioinformatics.scm (vg)[inputs]: Use curl instead of curl-minimal. Arun Isaac
2023-04-10Upgrade guix channel to a9a6432.Arun Isaac
2023-03-24Adding ruby-lmdb packagepjotrp
2023-03-24Adding ruby-lmdb packagepjotrp
2023-03-22bh20-seq-resource-container.scm updatesEfraim Flashner
2023-03-22python-rdflib-shim: Build with upstream python-rdflib-jsonld....* gn/packages/python.scm (python-rdflib-shim)[source]: Add snippet to use any version of python-rdflib-jsonld. [propagated-inputs]: Replace python-rdflib-jsonld-0.6.1 with python-rdflib-jsonld. (python-rdflib-jsonld-0.6.1): Remove variable. Efraim Flashner
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