From 859c6b7c31949feab84c6c91acaf1d1f2838d30c Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Thu, 21 Mar 2024 12:41:53 -0400 Subject: [PATCH 1/2] Run tests with 1.28, and add missing tool versions to sanitize allowlist --- .github/workflows/test.yaml | 2 +- galaxy/values.yaml | 14 ++++++++++++-- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index bbde0299..324e7ae7 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -34,7 +34,7 @@ jobs: - name: Start k8s locally uses: jupyterhub/action-k3s-helm@v3 with: - k3s-version: v1.25.15+k3s2 # releases: https://github.com/k3s-io/k3s/tags + k3s-version: v1.28.7+k3s1 # releases: https://github.com/k3s-io/k3s/tags metrics-enabled: false traefik-enabled: false - name: Verify function of k8s, kubectl, and helm diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 4c2ebae0..94c606b9 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -498,21 +498,31 @@ configs: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0 toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0 toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 - toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 + toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 + toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 + toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 + toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.44+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy2 + toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1 - toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1 + toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6 toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/5.0.5.0 + toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 + toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 + toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 + toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0 toolshed.g2.bx.psu.edu/repos/iuc/prestor_abseq3/prestor_abseq3/0.6.2+galaxy0 toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3 toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.1.0+galaxy0 + toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1 + toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 build_sites.yml: - type: ucsc From e81042cdb9751bc70d8f75c368dd765164a26ba6 Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Tue, 16 Apr 2024 16:09:13 -0500 Subject: [PATCH 2/2] Add plotly tools to allow list --- galaxy/values.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 94c606b9..710fdbb8 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -524,6 +524,9 @@ configs: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 + toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1 + toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2 + toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1 build_sites.yml: - type: ucsc file: "{{if .Values.refdata.enabled}}/cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt{{else}}/galaxy/server/tool-data/shared/ucsc/ucsc_build_sites.txt.sample{{end}}"