GitHub / nextstrain/docker-base issues and pull requests
#237 - Remove pangoLEARN and its dependencies
Pull Request -
State: closed - Opened by huddlej 8 months ago
#236 - Remove CVXOPT build
Pull Request -
State: closed - Opened by victorlin 9 months ago
- 1 comment
#235 - Add xlrd
Pull Request -
State: closed - Opened by huddlej 9 months ago
#234 - Build time for linux/arm64 image
Issue -
State: open - Opened by tsibley 9 months ago
- 3 comments
#233 - Upgrade base image from Debian Bullseye (oldstable) to Bookworm (stable)
Pull Request -
State: closed - Opened by tsibley 11 months ago
- 6 comments
#232 - Add the SQLite CLI for `augur merge`
Pull Request -
State: closed - Opened by tsibley 11 months ago
- 4 comments
#231 - Update to Snakemake version 8
Pull Request -
State: open - Opened by victorlin 11 months ago
#230 - Bump pathogen-embed to 3.0.0
Pull Request -
State: closed - Opened by huddlej 12 months ago
#229 - Bump pathogen-embed to 2.3.0
Pull Request -
State: closed - Opened by huddlej about 1 year ago
- 2 comments
#228 - Upgrade IQ-TREE to 2.3.5 with CMAPLE support
Pull Request -
State: closed - Opened by tsibley about 1 year ago
- 5 comments
#227 - Improve the process around pinning 3rd party tools
Issue -
State: open - Opened by victorlin about 1 year ago
- 2 comments
#226 - Add IQtree version with cmaple feature
Issue -
State: closed - Opened by corneliusroemer about 1 year ago
- 3 comments
Labels: enhancement
#225 - Update lassa CI
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
#224 - Update avian flu ci
Pull Request -
State: closed - Opened by jameshadfield about 1 year ago
- 1 comment
#223 - CI: Update test-pathogen-repo-ci
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
#222 - Build image based on conda-base?
Issue -
State: open - Opened by victorlin about 1 year ago
- 7 comments
Labels: proposal
#221 - Add pathogen-embed to the base image
Pull Request -
State: closed - Opened by huddlej about 1 year ago
- 3 comments
#220 - entrypoint-aws-batch: Upload .snakemake/metadata/ too
Pull Request -
State: closed - Opened by tsibley about 1 year ago
- 1 comment
#219 - Support Snakemake --report
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
#218 - Unable to use Snakemake `--report`
Issue -
State: closed - Opened by joverlee521 about 1 year ago
- 2 comments
Labels: bug
#217 - ci.yaml: Pin pathogen-repo-ci to v0
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
#216 - Revisit updating AWS CLI to v2
Issue -
State: open - Opened by joverlee521 about 1 year ago
- 1 comment
#215 - Isolate AWS CLI (v1) into its own Python venv
Pull Request -
State: closed - Opened by tsibley about 1 year ago
#214 - Use AWS CLI v2
Pull Request -
State: closed - Opened by joverlee521 about 1 year ago
- 1 comment
#213 - awscli `--no-sign-request` option not working
Issue -
State: closed - Opened by joverlee521 about 1 year ago
- 9 comments
#212 - Run IQ-TREE natively in ARM64 image
Issue -
State: open - Opened by victorlin about 1 year ago
- 1 comment
Labels: enhancement
#211 - Reference new CI target
Pull Request -
State: closed - Opened by victorlin over 1 year ago
#210 - Fix CI
Pull Request -
State: closed - Opened by victorlin over 1 year ago
#209 - Dockerfile: Upgrade csvtk to v0.30.0
Pull Request -
State: closed - Opened by joverlee521 over 1 year ago
#208 - ImportError of cvxopt, due to missing "liblapack.3.dylib"
Issue -
State: closed - Opened by kuangjizi over 1 year ago
- 1 comment
Labels: bug
#207 - ci: Remove python-version input to setup-nextstrain-cli action
Pull Request -
State: closed - Opened by tsibley over 1 year ago
#206 - Unpin Biopython
Pull Request -
State: closed - Opened by victorlin over 1 year ago
#205 - Temporarily disable zika CI
Pull Request -
State: closed - Opened by victorlin over 1 year ago
#204 - Use Nextclade v3
Pull Request -
State: closed - Opened by victorlin over 1 year ago
- 1 comment
#203 - Symlink default nextclade to nextclade3
Pull Request -
State: closed - Opened by corneliusroemer over 1 year ago
- 1 comment
#202 - Pin pulp<2.8 for snakemake
Pull Request -
State: closed - Opened by corneliusroemer over 1 year ago
- 2 comments
#201 - Update `nextclade3` to 3.0.0-alpha.2
Pull Request -
State: closed - Opened by corneliusroemer over 1 year ago
#200 - Pin Biopython 1.81
Pull Request -
State: closed - Opened by victorlin over 1 year ago
- 1 comment
#199 - Bump actions/upload-artifact from 3 to 4
Pull Request -
State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies
#198 - Upgrade nextclade to 3.0.0-alpha.1
Pull Request -
State: closed - Opened by ivan-aksamentov over 1 year ago
- 1 comment
#197 - Upgrade nextclade to 3.0.0-alpha.1
Pull Request -
State: closed - Opened by ivan-aksamentov over 1 year ago
- 1 comment
#196 - Bump actions/setup-python from 4 to 5
Pull Request -
State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies
#195 - Add Nextclade v3 alpha; remove Nextclade v1
Pull Request -
State: closed - Opened by ivan-aksamentov over 1 year ago
- 8 comments
#194 - Bump actions/github-script from 6 to 7
Pull Request -
State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies
#193 - Remove pyfastx build dependencies
Pull Request -
State: closed - Opened by victorlin over 1 year ago
#192 - Include Make in builder-target-platform image
Pull Request -
State: closed - Opened by tsibley over 1 year ago
- 2 comments
#191 - CI: Update mpox repo name
Pull Request -
State: closed - Opened by victorlin over 1 year ago
#190 - Use central action to setup Nextstrain CLI
Pull Request -
State: closed - Opened by victorlin over 1 year ago
- 1 comment
#189 - Update Node.js installation method
Pull Request -
State: closed - Opened by victorlin over 1 year ago
- 1 comment
#188 - CI failing: 404 when fetching nodejs_18.17.1-deb-1nodesource1_arm64.deb
Issue -
State: closed - Opened by victorlin almost 2 years ago
- 2 comments
Labels: bug
#187 - Install CVXOPT from PyPI on linux/arm64
Issue -
State: closed - Opened by victorlin almost 2 years ago
- 6 comments
Labels: blocked
#186 - Install jaxlib from PyPI on linux/arm64
Pull Request -
State: closed - Opened by victorlin almost 2 years ago
- 1 comment
#185 - Temporarily disable monkeypox CI
Pull Request -
State: closed - Opened by victorlin almost 2 years ago
#184 - Bump aws-actions/configure-aws-credentials from 2 to 4
Pull Request -
State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies
#183 - Bump docker/setup-qemu-action from 2 to 3
Pull Request -
State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies
#182 - Bump docker/login-action from 2 to 3
Pull Request -
State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies
#181 - Configure Nextstrain CLI to use the ambient runtime inside this runtime
Pull Request -
State: closed - Opened by tsibley almost 2 years ago
- 3 comments
#180 - Bump actions/checkout from 3 to 4
Pull Request -
State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies
#179 - Do not merge: Image for neherlab/BA286 workflow
Pull Request -
State: closed - Opened by corneliusroemer almost 2 years ago
- 2 comments
#178 - Add nano and vim-tiny for usability in interactive prompt
Pull Request -
State: open - Opened by corneliusroemer almost 2 years ago
- 1 comment
#177 - Include basic editor(s): nano and vi(m) [tiny or minimal]
Issue -
State: open - Opened by corneliusroemer almost 2 years ago
Labels: enhancement
#176 - Bump snakemake pin to 7.32.3
Pull Request -
State: closed - Opened by corneliusroemer almost 2 years ago
- 1 comment
#175 - Bump aws-actions/configure-aws-credentials from 2 to 3
Pull Request -
State: closed - Opened by dependabot[bot] almost 2 years ago
- 1 comment
Labels: dependencies
#174 - Add nextstrain/rsv to CI
Pull Request -
State: closed - Opened by victorlin almost 2 years ago
- 1 comment
#173 - Jax and jaxlib
Pull Request -
State: closed - Opened by joverlee521 about 2 years ago
- 6 comments
#172 - Add git to runtime dependencies
Pull Request -
State: closed - Opened by huddlej about 2 years ago
- 1 comment
#171 - Update jaxlib for evofr on linux/arm64
Pull Request -
State: closed - Opened by joverlee521 about 2 years ago
- 1 comment
#170 - Upgrade Node.js to v18
Pull Request -
State: closed - Opened by victorlin about 2 years ago
- 3 comments
#169 - Build CVXOPT in cached section
Pull Request -
State: closed - Opened by victorlin about 2 years ago
#168 - Summarize build execution times in CI
Pull Request -
State: closed - Opened by victorlin about 2 years ago
#167 - Transient errors copying from GHCR to Docker Hub
Issue -
State: closed - Opened by victorlin about 2 years ago
- 1 comment
Labels: bug
#166 - start-localhost-registry: Start container if it already exists
Pull Request -
State: closed - Opened by tsibley about 2 years ago
#165 - Omit dev deps when installing Auspice
Pull Request -
State: closed - Opened by tsibley about 2 years ago
- 4 comments
#164 - Consider using different registries
Issue -
State: closed - Opened by victorlin about 2 years ago
- 1 comment
Labels: enhancement, revisit sometime
#163 - Use skopeo for cleanup
Pull Request -
State: closed - Opened by victorlin about 2 years ago
- 1 comment
#162 - Provide native binaries for all programs on all platforms
Issue -
State: closed - Opened by victorlin about 2 years ago
- 2 comments
Labels: enhancement, revisit sometime
#161 - ci: Shellcheck
Pull Request -
State: closed - Opened by tsibley about 2 years ago
#160 - Improve storage for local dev
Pull Request -
State: closed - Opened by tsibley about 2 years ago
- 2 comments
#159 - Tests
Pull Request -
State: closed - Opened by tsibley about 2 years ago
- 1 comment
#158 - Envdir support
Pull Request -
State: closed - Opened by tsibley about 2 years ago
- 2 comments
#157 - Remove pangoLEARN
Issue -
State: closed - Opened by huddlej about 2 years ago
- 1 comment
Labels: enhancement
#156 - wip: fast build only amd64
Pull Request -
State: closed - Opened by corneliusroemer about 2 years ago
- 1 comment
#153 - Don't delete the GHCR package
Pull Request -
State: closed - Opened by victorlin about 2 years ago
- 1 comment
#145 - Update pinned software to latest
Pull Request -
State: open - Opened by corneliusroemer about 2 years ago
- 3 comments
#141 - Expose differences between platform-specific image variants
Issue -
State: closed - Opened by victorlin over 2 years ago
- 1 comment
Labels: enhancement, revisit sometime
#140 - Unable to resolve host for NCBI Datasets CLI FTP download
Issue -
State: closed - Opened by victorlin over 2 years ago
- 2 comments
#134 - Add treetime as direct pip3 install?
Issue -
State: closed - Opened by corneliusroemer over 2 years ago
- 8 comments
Labels: proposal
#131 - CI: Transient 403 Forbidden errors when pushing to ghcr.io
Issue -
State: closed - Opened by victorlin over 2 years ago
- 7 comments
#130 - CI: Validate images across platforms
Pull Request -
State: closed - Opened by victorlin over 2 years ago
- 9 comments
#129 - Re-evaluate the way some Nextstrain components are added
Issue -
State: closed - Opened by victorlin over 2 years ago
- 8 comments
Labels: proposal
#128 - Different Augur versions between amd64 and arm64 images
Issue -
State: closed - Opened by victorlin over 2 years ago
- 20 comments
Labels: bug
#127 - Use Ubuntu packages for FastTree and other programs?
Issue -
State: open - Opened by victorlin over 2 years ago
- 6 comments
Labels: proposal
#122 - Upgrade to Node.js 16
Pull Request -
State: closed - Opened by victorlin over 2 years ago
- 4 comments
#119 - Install jaxlib from a Nextstrain-managed repository
Issue -
State: closed - Opened by victorlin over 2 years ago
- 5 comments
Labels: enhancement
#101 - Split CI into separate jobs using artifact upload/download
Pull Request -
State: closed - Opened by victorlin almost 3 years ago
- 1 comment
#100 - Upgrade python & debian to the latest released version
Pull Request -
State: closed - Opened by jgadling almost 3 years ago
- 3 comments
#99 - MAFFT: current version has a bug in the FFT-NS-i / --auto options
Issue -
State: open - Opened by victorlin almost 3 years ago
- 1 comment
Labels: bug
#98 - Use cross-compilation where possible
Pull Request -
State: closed - Opened by victorlin almost 3 years ago
#97 - Test whether re-installing GMP improves execution time of long-running workflows
Issue -
State: open - Opened by victorlin almost 3 years ago
- 3 comments
Labels: enhancement
#96 - Improve Node.js installation
Pull Request -
State: closed - Opened by victorlin almost 3 years ago
- 1 comment