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2023-08-31Downgrade guix to a4e9842.Arun Isaac
2023-08-31Revert "Pin guix-bioinformatics to commit with Python-3.9"Arun Isaac
This reverts commit 0d743eb249bbdb67009d23ee53b2ee0ae881f725.
2023-08-31Pin guix-bioinformatics to commit with Python-3.9Frederick Muriuki Muriithi
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
2023-08-30Replace `(...) with (list ...): Fixes "undefined gexp" failure.Frederick Muriuki Muriithi
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
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.Arun Isaac
tissue is now in upstream Guix. * gn/packages/gemini.scm: Delete file.
2023-07-05gn: genenetwork3: Update to 0.1.0-3.f52247c.Arun Isaac
* gn/packages/genenetwork.scm (genenetwork3): Update to 0.1.0-3.f52247c.
2023-07-05Run genenetwork3 tests using pytest.Arun Isaac
* gn/packages/genenetwork.scm (genenetwork3)[arguments]: Replace check phase to use pytest.
2023-07-04Remove deprecated #:asd-files argument.Arun Isaac
* 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.
2023-06-29Upgrade guix channel to d4e9ad2.Arun Isaac
2023-06-29 gn: gemma: Fix build using latest gccpjotrp
2023-06-26Fix DirsAllowed parameterMunyoki Kilyungi
* gn/services/databases.scm (virtuoso-shepherd-service): Remove square brackets that sorround the DirsAllowed parameter.
2023-06-26Merge branch 'add-virtuoso-allowed-dirs' into 'master'BonfaceKilz
Add dirs-allowed to virtuoso configs See merge request genenetwork/guix-bioinformatics!24
2023-06-23Fix indentation.Arun Isaac
* .guix-channel: Fix indentation.
2023-06-22Fix "channel dependency has an invalid introduction field" errorMunyoki Kilyungi
* .guix-channel: Update how channel dependencies are defined to match: https://guix.gnu.org/manual/en/html_node/Declaring-Channel-Dependencies.html
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.Efraim Flashner
* 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.
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.Arun Isaac
curl-minimal has been removed from upstream Guix. * gn/packages/bioinformatics.scm (vg)[inputs]: Use curl instead of curl-minimal.
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.Efraim Flashner
* 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.
2023-03-22bh20-seq-resource: Add version without profile collisions.Efraim Flashner
* gn/packages/bioinformatics.scm (bh20-seq-resource-for-service): New variable. * gn/services/bh20-seq-resource-container.scm (covid19-pubseq-configuration): Use it by default.
2023-03-22bh20-seq-resource: Patch reference to minimap2.Efraim Flashner
* gn/packages/bioinformatics.scm (bh20-seq-resource)[arguments]: Add phase to hardcode path to minimap2. [inputs]: Add minimap2.
2023-03-22bh20-seq-resource: Update to 1.0-4.2ae7191.Efraim Flashner
* gn/packages/bioinformatics.scm (bh20-seq-resource): Update to 1.0-4.2ae7191. [source]: Adjust snippet for changes in source. [arguments]: Skip tests. [propagated-inputs]: Add python-shexc-0.7. Remove python-dateutil, python-flask, python-pycurl, python38-ruaml.yaml-0.15.76, clustalw, python-twint. [native-inputs]: Remove git, python-oauth2client, python-uritemplate. Replace python-pytest-4 with python-pytest-5, python-pytest-runner-2 with python-pytest-runner-4.
2023-03-22Add python-pytest-runner-4.Efraim Flashner
* gn/packages/python.scm (python-pytest-runner-4): New variable. * gn/packages/bioinformatics.scm (python-pytest-runner-2): MOve to python.scm
2023-03-22fixup python-pyshexcEfraim Flashner
2023-03-22python-pyshex: Downgrade to 0.7.14.Efraim Flashner
* gn/packages/python.scm (python-pyshex): Downgrade to 0.7.14. [arguments]: Disable tests. Add phase to fix compatibility with rdflib-6. Adjust custom 'check phase. [propagated-inputs]: Remove python-chardet. Replace python-pyshexc with python-pyshexc-0.7, python-rdflib-shim with python-rdflib, python-sparqlsluper with python-sparql-slurper.
2023-03-22Add python-py-dateutil.Efraim Flashner
* gn/packages/python.scm (python-py-dateutil): New variable.
2023-03-22Add python-pyshexc-0.7.Efraim Flashner
* gn/packages/python.scm (python-pyshexc-0.7): New variable.
2023-03-22Add python-pytest-5.Efraim Flashner
* gn/packages/python.scm (python-pytest-5): New variable.
2023-03-20python-arvados-python-client: Update to 2.5.0.Efraim Flashner
* gn/packages/python.scm (python-arvados-python-client): Update to 2.5.0. [source]: Add snippet to not limit the maximum version of pycurl. [propagated-inputs]: Add python-google-api-core-1, python-google-auth-1, python-protobuf, python-pyparsing-2.4.7, python-ruamel.yaml. Remove python38-ruaml.yaml-0.15.76, python-setuptools, python-oauth2client, python-uritemplate. (python38-ruaml.yaml-0.15.76): Remove variable.
2023-03-20python-shexjsg: Update to 0.8.2.Efraim Flashner
* gn/packages/python.scm (python-shexjsg): Update to 0.8.2. [arguments]: Remove custom 'patch-source phase. Update custom 'check phase. [propagated-inputs]: Remove python-antlr4-python3-runtime, python-certifi, python-chardet, python-idna, python-isodate, python-requests, python-urllib3. [native-inputs]: Add python-rdflib-shim, python-requests. Remove python-pyparsing, python-pyshexc, python-rdflib, python-rdflib-jsonld, python-six, custom test-suite git checkout.
2023-03-20Add python-sparqlslurper.Efraim Flashner
* gn/packages/python.scm (python-sparqlslurper): New variable.
2023-03-20Add python-rdflib-shim.Efraim Flashner
* gn/packages/python.scm (python-rdflib-shim): New variable. (python-rdflib-jsonld-0.6.1): New variable.
2023-03-20python-pyshex: Update to 0.8.1.Efraim Flashner
* gn/packages/python.scm (python-pyshex): Update to 0.8.1. [arguments]: Remove custom 'patch-source phase. Update custom 'check phase. [propagated-inputs]: Add python-chardet, python-rdflib-shim, python-sparqlslurper. Remove python-rdflib, python-rdflib-jsonld, python-pbr, python-sparql-slurper. [native-inputs]: Add python-pbr, python-unitttest2.
2023-03-20python-pyshexc: Update to 0.9.1.Efraim Flashner
* gn/packages/python.scm (python-pyshexc): Update to 0.9.1. [arguments]: Update custom 'check phase. [propagated-inputs]: Add python-chardet, python-rdflib-shim, python-shexjsg. Remove python-rdflib, python-rdflib-jsonld, python-requests. [native-inputs]: Add python-pbr, python-requests. Remove python-shexjsg, custom test-suite git checkout. (python-shexjsg-min): Remove variable.
2023-03-19python-pyjsg: Update to 0.11.10.Efraim Flashner
* gn/packages/python.scm (python-pyjsg): Update to 0.11.10. [arguments]: Remove 'patch-source phase. Skip 1 set of tests in custom 'check phase. [propagated-inputs]: Move python-requests ... [native-inputs]: ... to here. Add python-unittest2. Remove test-suite checkout.
2023-03-19python-antlr4-python3-runtime: Update to 4.9.3.Efraim Flashner
* gn/packages/python.scm (python-antlr4-python3-runtime): Update to 4.9.3.
2023-03-19python-pytest-4: Add missing input.Efraim Flashner
* gn/packages/python.scm (python-pytest-4)[native-inputs]: Add python-atomicwrites.
2023-03-19updates to julia packagesEfraim Flashner
2023-03-08gn: genenetwork3: Add python-argon-cffiFrederick Muriuki Muriithi
As part of improving the security of passwords, this commit adds python-argon-cffi that enables use of the better Argon2 password hashing algorithm, rather than the dated bcrypt that is a tad vulnerable to offline cracking.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-15 06:46:53 +0000