From 4e27f15ed2ec1c526cccc66c6010e0804688e6c0 Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Fri, 13 Aug 2021 19:16:32 -0400 Subject: [PATCH 01/25] Changes for not mounting entire NFS to each job friends with https://github.com/galaxyproject/galaxy/pull/12345 --- galaxy/values.yaml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 8cfd4e97..02eb3105 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -273,11 +273,20 @@ configs: k8s: load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner k8s_use_service_account: true - k8s_persistent_volume_claims: |- + k8s_data_volume_claim: |- {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}} + k8s_persistent_volume_claims: |- + {{ template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache, + {{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config, + {{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps, + {{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache, + {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp, + {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data, + {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools, + {{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index {{- if .Values.cvmfs.enabled -}} {{- range $key, $entry := .Values.cvmfs.galaxyPersistentVolumeClaims -}} - ,{{- template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}} + ,{{ template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}} {{- end -}} {{- end -}} {{- if .Values.initJob.downloadToolConfs.enabled -}} From bb53d371a72ba298a64f16d17328b26584608388 Mon Sep 17 00:00:00 2001 From: Alexandru Mahmoud Date: Mon, 30 Aug 2021 15:47:42 -0400 Subject: [PATCH 02/25] Separate data and working dir pvcs --- galaxy/values.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 02eb3105..fb569a81 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -275,6 +275,8 @@ configs: k8s_use_service_account: true k8s_data_volume_claim: |- {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}} + k8s_working_volume_claim: |- + {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}} k8s_persistent_volume_claims: |- {{ template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache, {{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config, From 380430dd51ada4def02cafcdc7733d5bccc5adce Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Mon, 20 Dec 2021 19:29:32 +0530 Subject: [PATCH 03/25] Removed unnecessary mounts and made inputs read only --- galaxy/values.yaml | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/galaxy/values.yaml b/galaxy/values.yaml index fb569a81..fe0ef196 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -274,18 +274,14 @@ configs: load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner k8s_use_service_account: true k8s_data_volume_claim: |- - {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}} + {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}:r k8s_working_volume_claim: |- {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}} k8s_persistent_volume_claims: |- - {{ template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache, - {{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config, - {{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps, - {{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache, - {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp, - {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data, - {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools, - {{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index + {{ template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config:r, + {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp:rw, + {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data:r, + {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools:r {{- if .Values.cvmfs.enabled -}} {{- range $key, $entry := .Values.cvmfs.galaxyPersistentVolumeClaims -}} ,{{ template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}} From fce1ae63ea88b510d0d59d659614ee772c499ddb Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:17:18 +0530 Subject: [PATCH 04/25] Add short link to the TPV shared database --- galaxy/values.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 9c85c0c0..8ec05fbf 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -422,7 +422,7 @@ configs: rules_module: tpv.rules docker_default_container_id: "{{ .Values.image.repository }}:{{ .Values.image.tag }}" tpv_config_files: - - https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml + - https://gxy.io/tpv/db.yml - lib/galaxy/jobs/rules/tpv_rules_local.yml # limits: # - type: registered_user_concurrent_jobs From 9905ab2dca399eb44c07bf80c3efc98799195e81 Mon Sep 17 00:00:00 2001 From: Matt Pawelczyk Date: Thu, 15 Feb 2024 16:37:44 +0100 Subject: [PATCH 05/25] Exposes job.PriorityClass.value as modifiable value --- galaxy/templates/priorityclass-job.yaml | 8 ++++++-- galaxy/values.yaml | 1 + 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/galaxy/templates/priorityclass-job.yaml b/galaxy/templates/priorityclass-job.yaml index 1d5e2b24..980ebbdb 100644 --- a/galaxy/templates/priorityclass-job.yaml +++ b/galaxy/templates/priorityclass-job.yaml @@ -5,8 +5,12 @@ metadata: name: {{ include "galaxy.pod-priority-class" . }} labels: {{- include "galaxy.labels" . | nindent 4 }} -value: -1000 +value: {{ if .Values.jobs.priorityClass.value -}} + {{ .Values.jobs.priorityClass.value}} + {{- else -}} + -1000 + {{- end}} preemptionPolicy: Never globalDefault: false -description: "Galaxy jobs will run when cluster resources are available and will not preempt existing workloads." +description: "Galaxy jobs will not preempt existing workloads and depending on the value spin up new resources for the computation." {{ end }} diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 8ec05fbf..4c2ebae0 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -542,6 +542,7 @@ jobs: #- Assign a [priorityClass](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/#priorityclass) to the dispatched jobs. enabled: true existingClass: "" + value: -1000 rules: tpv_rules_local.yml: global: From 4ed41b3bd978f55c32e92d42def86ba0a2141ccc Mon Sep 17 00:00:00 2001 From: Matt Pawelczyk <125464188+mapk-amazon@users.noreply.github.com> Date: Thu, 15 Feb 2024 17:20:00 +0100 Subject: [PATCH 06/25] Update galaxy/templates/priorityclass-job.yaml Updated description according to afgane's input. Co-authored-by: Enis Afgan --- galaxy/templates/priorityclass-job.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/templates/priorityclass-job.yaml b/galaxy/templates/priorityclass-job.yaml index 980ebbdb..31220a6e 100644 --- a/galaxy/templates/priorityclass-job.yaml +++ b/galaxy/templates/priorityclass-job.yaml @@ -12,5 +12,5 @@ value: {{ if .Values.jobs.priorityClass.value -}} {{- end}} preemptionPolicy: Never globalDefault: false -description: "Galaxy jobs will not preempt existing workloads and depending on the value spin up new resources for the computation." +description: "By default, Galaxy jobs will not preempt existing workloads but will run when cluster resources are available. Depending on the cluster setup, the preemption value can be modified to prompt scaling of the cluster for the computation." {{ end }} From dcf177094bb0556860edb74e57d7a47fcfb2d828 Mon Sep 17 00:00:00 2001 From: Matt Pawelczyk <125464188+mapk-amazon@users.noreply.github.com> Date: Thu, 15 Feb 2024 17:37:48 +0100 Subject: [PATCH 07/25] Update galaxy/templates/priorityclass-job.yaml Simplifying if/else by default as suggested by nuwang. Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> --- galaxy/templates/priorityclass-job.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/galaxy/templates/priorityclass-job.yaml b/galaxy/templates/priorityclass-job.yaml index 31220a6e..36a73936 100644 --- a/galaxy/templates/priorityclass-job.yaml +++ b/galaxy/templates/priorityclass-job.yaml @@ -5,11 +5,7 @@ metadata: name: {{ include "galaxy.pod-priority-class" . }} labels: {{- include "galaxy.labels" . | nindent 4 }} -value: {{ if .Values.jobs.priorityClass.value -}} - {{ .Values.jobs.priorityClass.value}} - {{- else -}} - -1000 - {{- end}} +value: {{ default "-1000" .Values.jobs.priorityClass.value -}} preemptionPolicy: Never globalDefault: false description: "By default, Galaxy jobs will not preempt existing workloads but will run when cluster resources are available. Depending on the cluster setup, the preemption value can be modified to prompt scaling of the cluster for the computation." From cdd1f393861274e9da7e1deb1c5b1fac8bf36616 Mon Sep 17 00:00:00 2001 From: Matt Pawelczyk <125464188+mapk-amazon@users.noreply.github.com> Date: Thu, 15 Feb 2024 17:45:16 +0100 Subject: [PATCH 08/25] Update galaxy/templates/priorityclass-job.yaml Fixing last line chomp. Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> --- galaxy/templates/priorityclass-job.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/templates/priorityclass-job.yaml b/galaxy/templates/priorityclass-job.yaml index 36a73936..df518387 100644 --- a/galaxy/templates/priorityclass-job.yaml +++ b/galaxy/templates/priorityclass-job.yaml @@ -5,7 +5,7 @@ metadata: name: {{ include "galaxy.pod-priority-class" . }} labels: {{- include "galaxy.labels" . | nindent 4 }} -value: {{ default "-1000" .Values.jobs.priorityClass.value -}} +value: {{ default "-1000" .Values.jobs.priorityClass.value }} preemptionPolicy: Never globalDefault: false description: "By default, Galaxy jobs will not preempt existing workloads but will run when cluster resources are available. Depending on the cluster setup, the preemption value can be modified to prompt scaling of the cluster for the computation." From b66b2bf11c9e1ea3fbb834e0c64aa0558374b7f4 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 16 Feb 2024 04:40:46 +0000 Subject: [PATCH 09/25] Automatic Version Bumping from 5.8.0 to 5.9.0 --- galaxy/Chart.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml index ae6c4aa8..572b68bb 100644 --- a/galaxy/Chart.yaml +++ b/galaxy/Chart.yaml @@ -1,7 +1,7 @@ apiVersion: v2 name: galaxy type: application -version: 5.8.0 +version: 5.9.0 appVersion: "23.1" description: Chart for Galaxy, an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. icon: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png From 29f01e62b8e79091a7d289bc15b8151d20a086d0 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Mon, 19 Feb 2024 12:48:27 -0500 Subject: [PATCH 10/25] Ensure that one of the dependent jobs succeeded. --- .github/workflows/packaging.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml index 4064be71..8700be98 100644 --- a/.github/workflows/packaging.yml +++ b/.github/workflows/packaging.yml @@ -51,6 +51,10 @@ jobs: needs: [ package-from-pr, package-from-manual ] name: Create a tag and GitHub release for this version. runs-on: ubuntu-latest + if: | + always() + && contains(needs.*.result, 'success') + && !contains(needs.*.result, 'failure') steps: - name: Tag and release run: | From 0a2fdd85eba59aedc59ecf49fd1b8b73ab1cfe76 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Tue, 20 Feb 2024 13:14:50 -0500 Subject: [PATCH 11/25] Mark the last release as the --latest --- .github/workflows/packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml index 8700be98..7436a068 100644 --- a/.github/workflows/packaging.yml +++ b/.github/workflows/packaging.yml @@ -61,4 +61,4 @@ jobs: version=v$(cat galaxy/Chart.yaml | grep ^version: | awk '{print $2}') git tag -a $version -m "Automatic release of $version" git push origin $version - gh release create $version --generate-notes + gh release create $version --generate-notes --latest From 24920ed1772cd802404563456895b1c386bf288c Mon Sep 17 00:00:00 2001 From: nuwang <2070605+nuwang@users.noreply.github.com> Date: Wed, 21 Feb 2024 00:12:38 +0530 Subject: [PATCH 12/25] Add more notes on product deployments and chart installations --- README.md | 47 +++++++++++++++++++++++++---------------------- 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 3c150f37..f7684f85 100644 --- a/README.md +++ b/README.md @@ -34,18 +34,40 @@ helm upgrade --install ingress-nginx ingress-nginx \ This chart relies on the features of other charts for common functionality: - [postgres-operator](https://github.com/zalando/postgres-operator) for the database; -- [CSI-S3 chart](https://github.com/ctrox/csi-s3/pull/75/) for linking the - reference data to Galaxy and jobs based on S3FS. +- [galaxy-cvmfs-csi](https://github.com/CloudVE/galaxy-cvmfs-csi-helm) for linking the + reference data to Galaxy and jobs based on CVMFS (default). +- [csi-s3](https://github.com/ctrox/csi-s3/pull/75/) for linking + reference data to Galaxy and jobs based on S3FS (optional/alternative to CVMFS). +- [rabbitmq-cluster-operator](https://github.com/rabbitmq/cluster-operator) for deploying + the message queue. In a production setting, especially if the intention is to run multiple Galaxies in a single cluster, we recommend installing the dependency charts separately once per cluster, and installing Galaxy with `--set postgresql.deploy=false ---set s3csi.deploy=false`. +--set s3csi.deploy=false --set cvmfs.deploy=false --set rabbitmq.deploy=false`. --- ## Installing the chart +### Using the chart from the packaged chart repo + +1. The chart is automatically packaged, versioned and uploaded to a helm repository +on each accepted PR. Therefore, the latest version of the chart can be downloaded +from this repository. + +```console +helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/ +helm repo update +``` + +2. Install the chart with the release name `my-galaxy`. It is not advisable to + install Galaxy in the `default` namespace. + +```console +helm install my-galaxy-release cloudve/galaxy +``` + ### Using the chart from GitHub repo 1. Clone this repository and add required dependency charts: @@ -68,25 +90,6 @@ In several minute, Galaxy will be available at `/galaxy/` URL of your Kubernetes cluster. If you are running the development Kubernetes, Galaxy will be available at `http://localhost/galaxy/` (note the trailing slash). -### Using the chart from the packaged chart repo - -1. Instead of using the source code repo, you can install the packaged version -of the chart and hence not need to clone this GitHub repo. The packaged version -may contain a bit older but possibly more stable code than what is the GitHub -repo at any a given point in time. - -```console -helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/ -helm repo update -``` - -2. Install the chart with the release name `my-galaxy`. It is not advisable to - install Galaxy in the `default` namespace. - -```console -helm install my-galaxy-release cloudve/galaxy -``` - ## Uninstalling the chart To uninstall/delete the `my-galaxy` deployment, run: From 54d93c86677415af0004e132d7d7f0ba14108421 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Wed, 21 Feb 2024 16:56:32 -0500 Subject: [PATCH 13/25] This is the script I have been using to tag and release prior versions. --- scripts/tag-and-release.sh | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100755 scripts/tag-and-release.sh diff --git a/scripts/tag-and-release.sh b/scripts/tag-and-release.sh new file mode 100755 index 00000000..52981968 --- /dev/null +++ b/scripts/tag-and-release.sh @@ -0,0 +1,26 @@ +#!/usr/bin/env bash + +# Date since the last release. We will search for commits newer than this. +# TODO There is probably some Git magic we could do to figure this out +SINCE=${SINCE:-2023-08-19} + +# The last version that was tagged. +# TODO There is probably some Git magic we could do to figure this out +LATEST=${LATEST:-5.7.6} + +# Search the git log for commits that did an Automatic version bump. +git log --oneline --grep=Automatic --since=$SINCE | awk '{print $1,$NF}' | grep -v $LATEST | tail -r | while read -r line ; do + commit=$(echo $line | awk '{print $1}') + tag=v$(echo $line | awk '{print $2}') + # Get the actual date the commit was made + export GIT_COMMITTER_DATE=$(git show --format=%aD $commit | head -1) + # Tag the commit + echo "Tagging $commit as $tag $GIT_COMMITTER_DATE" + git checkout $commit + git tag -a -m "Automatic tagging of $tag" $tag + git push origin $tag + # Generate the release. + gh release create $tag --generate-notes --latest +done +git checkout master +echo "Done." \ No newline at end of file From ba4a0e98e104b021ee7f771279b6ee447afac110 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Thu, 22 Feb 2024 22:10:26 -0500 Subject: [PATCH 14/25] Generate notes and command line parsing --- scripts/tag-and-release.sh | 68 ++++++++++++++++++++++++++++++++++---- 1 file changed, 62 insertions(+), 6 deletions(-) diff --git a/scripts/tag-and-release.sh b/scripts/tag-and-release.sh index 52981968..a4fc62f9 100755 --- a/scripts/tag-and-release.sh +++ b/scripts/tag-and-release.sh @@ -1,12 +1,67 @@ #!/usr/bin/env bash -# Date since the last release. We will search for commits newer than this. -# TODO There is probably some Git magic we could do to figure this out -SINCE=${SINCE:-2023-08-19} +# Determine our name for use in the help message. +SCRIPT=$(basename $(realpath $0)) + +# ANSI color codes for the console. +reset="\033[0m" +bold="\033[1m" +ital="\033[3m" # does not work on OS X + +# Function used to highlight text. +function hi() { + echo -e "$bold$@$reset" +} # The last version that was tagged. -# TODO There is probably some Git magic we could do to figure this out -LATEST=${LATEST:-5.7.6} +LATEST=$(git describe --tags `git rev-list --tags --max-count=1` | tr -d 'v') + +# Date since the last release. We will search for commits newer than this. +SINCE=$(git log -1 --format=%as v$LATEST) + +function help() { + less -RX << EOF + +$(hi NAME) + $SCRIPT + +$(hi DESCRIPTION) + Tags and generates a GitHub release for all commits that have "Automatic" in the + commit messages. These will be the commits that were generated by the packaging + GitHub action. + +$(hi SYNOPSIS) + $SCRIPT --size DATE --latest TAG_NAME + +$(hi OPTIONS) + -l|--latest the tag name of the last commit that was tagged. Default to $LATEST + -s|--since search the git log after this date (YYYY-MM-DD). Defaults to $SINCE + -h|--help prints this help message and exits + + The $(hi --latest) and $(hi --since) fields will be determined from the Git log + if they are not provided. + +EOF +} + +while [[ $# > 0 ]] ; do + case $1 in + -l|--latest) + LATEST=$2 + shift + ;; + -s|--since) + SINCE=$2 + shift + ;; + -h|--help|help) + help + exit + ;; + esac + shift +done +PREVIOUS="v$LATEST" # Search the git log for commits that did an Automatic version bump. git log --oneline --grep=Automatic --since=$SINCE | awk '{print $1,$NF}' | grep -v $LATEST | tail -r | while read -r line ; do @@ -20,7 +75,8 @@ git log --oneline --grep=Automatic --since=$SINCE | awk '{print $1,$NF}' | grep git tag -a -m "Automatic tagging of $tag" $tag git push origin $tag # Generate the release. - gh release create $tag --generate-notes --latest + gh release create $tag --generate-notes --latest --notes-start-tag $PREVIOUS + PREVIOUS=$tag done git checkout master echo "Done." \ No newline at end of file From 5752ec697382bde7fdec734789fe694e906380ed Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Thu, 22 Feb 2024 22:24:52 -0500 Subject: [PATCH 15/25] Add Press Q to quit to the help message --- scripts/tag-and-release.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/scripts/tag-and-release.sh b/scripts/tag-and-release.sh index a4fc62f9..1d2771f2 100755 --- a/scripts/tag-and-release.sh +++ b/scripts/tag-and-release.sh @@ -41,6 +41,8 @@ $(hi OPTIONS) The $(hi --latest) and $(hi --since) fields will be determined from the Git log if they are not provided. +Press $(hi Q) to quit this help. + EOF } From 1f4240d1b7b82302cc1ec33a1a5a314a3c7c37ce Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Fri, 23 Feb 2024 06:47:09 -0500 Subject: [PATCH 16/25] Fix typo in help. Handle invalid options --- scripts/tag-and-release.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/scripts/tag-and-release.sh b/scripts/tag-and-release.sh index 1d2771f2..0a110ada 100755 --- a/scripts/tag-and-release.sh +++ b/scripts/tag-and-release.sh @@ -31,7 +31,7 @@ $(hi DESCRIPTION) GitHub action. $(hi SYNOPSIS) - $SCRIPT --size DATE --latest TAG_NAME + $SCRIPT --since DATE --latest TAG_NAME $(hi OPTIONS) -l|--latest the tag name of the last commit that was tagged. Default to $LATEST @@ -60,6 +60,10 @@ while [[ $# > 0 ]] ; do help exit ;; + *) + echo "Invalid option $1" + echo "Run $(hi $SCRIPT help) for usage information" + exit esac shift done From b058b5e2ce1cec54148cccb68805fb755dc35890 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Wed, 13 Mar 2024 16:06:07 -0400 Subject: [PATCH 17/25] Add YAML document separators (triple dashes) to the start of yaml templates. --- galaxy/templates/configmap-cvmfs-fix.yaml | 1 + galaxy/templates/configmap-extra-files.yaml | 5 ++--- galaxy/templates/configmap-galaxy-rules.yaml | 1 + galaxy/templates/configmap-grafana-dashboard.yaml | 1 + galaxy/templates/configmap-nginx.yaml | 1 + galaxy/templates/configs-galaxy.yaml | 1 + galaxy/templates/cronjob-maintenance.yaml | 1 + galaxy/templates/deployment-celery-beat.yaml | 1 + galaxy/templates/deployment-celery.yaml | 1 + galaxy/templates/deployment-job.yaml | 2 +- galaxy/templates/deployment-metrics.yaml | 1 + galaxy/templates/deployment-nginx.yaml | 1 + galaxy/templates/deployment-tusd.yaml | 1 + galaxy/templates/deployment-web.yaml | 1 + galaxy/templates/deployment-workflow.yaml | 1 + galaxy/templates/hook-cvmfs-fix.yaml | 1 + galaxy/templates/ingress-activity-canary.yaml | 3 ++- galaxy/templates/ingress-tusd.yaml | 3 ++- galaxy/templates/ingress.yaml | 2 +- galaxy/templates/jobs-init.yaml | 1 + galaxy/templates/priorityclass-job.yaml | 1 + galaxy/templates/pv-s3fs.yaml | 1 + galaxy/templates/pvc-galaxy.yaml | 2 +- galaxy/templates/pvc-refdata.yaml | 2 +- galaxy/templates/rabbitmqcluster.yaml | 1 + galaxy/templates/rbac-job.yaml | 1 + galaxy/templates/secret-galaxy.yaml | 1 + galaxy/templates/service-galaxy.yaml | 1 + galaxy/templates/service-nginx.yaml | 1 + galaxy/templates/service-tusd.yaml | 1 + galaxy/templates/serviceaccount.yaml | 1 + 31 files changed, 34 insertions(+), 9 deletions(-) diff --git a/galaxy/templates/configmap-cvmfs-fix.yaml b/galaxy/templates/configmap-cvmfs-fix.yaml index d5d4c129..f680f119 100644 --- a/galaxy/templates/configmap-cvmfs-fix.yaml +++ b/galaxy/templates/configmap-cvmfs-fix.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 kind: ConfigMap metadata: diff --git a/galaxy/templates/configmap-extra-files.yaml b/galaxy/templates/configmap-extra-files.yaml index b0e60f60..53dc516c 100644 --- a/galaxy/templates/configmap-extra-files.yaml +++ b/galaxy/templates/configmap-extra-files.yaml @@ -1,5 +1,6 @@ {{- range $key, $entry := .Values.extraFileMappings -}} {{- if $entry }} +--- apiVersion: v1 metadata: # Extract the filename portion only @@ -20,9 +21,9 @@ data: {{- else }} {{- $entry.content | nindent 4 }} {{- end }} ---- {{- end }} {{- end }} +--- apiVersion: v1 metadata: name: {{ include "galaxy.fullname" $ }}-probedb-py @@ -32,5 +33,3 @@ kind: ConfigMap data: probedb.py: | {{- (.Files.Get "scripts/probedb.py") | nindent 4 }} - ---- diff --git a/galaxy/templates/configmap-galaxy-rules.yaml b/galaxy/templates/configmap-galaxy-rules.yaml index aaa5101c..ed09bb95 100644 --- a/galaxy/templates/configmap-galaxy-rules.yaml +++ b/galaxy/templates/configmap-galaxy-rules.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 kind: ConfigMap metadata: diff --git a/galaxy/templates/configmap-grafana-dashboard.yaml b/galaxy/templates/configmap-grafana-dashboard.yaml index 58d573aa..1ced09bb 100644 --- a/galaxy/templates/configmap-grafana-dashboard.yaml +++ b/galaxy/templates/configmap-grafana-dashboard.yaml @@ -1,4 +1,5 @@ {{- if .Values.influxdb.enabled }} +--- apiVersion: v1 kind: ConfigMap metadata: diff --git a/galaxy/templates/configmap-nginx.yaml b/galaxy/templates/configmap-nginx.yaml index d1166b32..a74409cd 100644 --- a/galaxy/templates/configmap-nginx.yaml +++ b/galaxy/templates/configmap-nginx.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 kind: ConfigMap metadata: diff --git a/galaxy/templates/configs-galaxy.yaml b/galaxy/templates/configs-galaxy.yaml index f1b0e229..4fa8a7ec 100644 --- a/galaxy/templates/configs-galaxy.yaml +++ b/galaxy/templates/configs-galaxy.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 metadata: name: {{ include "galaxy.fullname" . }}-configs diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml index 17b0219a..80deecd5 100644 --- a/galaxy/templates/cronjob-maintenance.yaml +++ b/galaxy/templates/cronjob-maintenance.yaml @@ -1,3 +1,4 @@ +--- apiVersion: batch/v1 kind: CronJob metadata: diff --git a/galaxy/templates/deployment-celery-beat.yaml b/galaxy/templates/deployment-celery-beat.yaml index e50a9622..0f46248d 100644 --- a/galaxy/templates/deployment-celery-beat.yaml +++ b/galaxy/templates/deployment-celery-beat.yaml @@ -1,3 +1,4 @@ +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/deployment-celery.yaml b/galaxy/templates/deployment-celery.yaml index c21660f4..100b4ac6 100644 --- a/galaxy/templates/deployment-celery.yaml +++ b/galaxy/templates/deployment-celery.yaml @@ -1,3 +1,4 @@ +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/deployment-job.yaml b/galaxy/templates/deployment-job.yaml index 28e12dc3..29988bd1 100644 --- a/galaxy/templates/deployment-job.yaml +++ b/galaxy/templates/deployment-job.yaml @@ -1,4 +1,5 @@ {{- range $handler_num, $e := until (int $.Values.jobHandlers.replicaCount) }} +--- apiVersion: apps/v1 kind: Deployment metadata: @@ -210,5 +211,4 @@ spec: tolerations: {{- toYaml . | nindent 8 }} {{- end }} ---- {{- end }} diff --git a/galaxy/templates/deployment-metrics.yaml b/galaxy/templates/deployment-metrics.yaml index 3f29b7b6..03637c43 100644 --- a/galaxy/templates/deployment-metrics.yaml +++ b/galaxy/templates/deployment-metrics.yaml @@ -1,4 +1,5 @@ {{- if .Values.metrics.enabled }} +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/deployment-nginx.yaml b/galaxy/templates/deployment-nginx.yaml index 34020fcb..36d0bb6d 100644 --- a/galaxy/templates/deployment-nginx.yaml +++ b/galaxy/templates/deployment-nginx.yaml @@ -1,3 +1,4 @@ +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/deployment-tusd.yaml b/galaxy/templates/deployment-tusd.yaml index 45813ab9..0d7d2fb7 100644 --- a/galaxy/templates/deployment-tusd.yaml +++ b/galaxy/templates/deployment-tusd.yaml @@ -1,4 +1,5 @@ {{ if .Values.tusd.enabled -}} +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/deployment-web.yaml b/galaxy/templates/deployment-web.yaml index 0a1f8c49..783d1a52 100644 --- a/galaxy/templates/deployment-web.yaml +++ b/galaxy/templates/deployment-web.yaml @@ -1,3 +1,4 @@ +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/deployment-workflow.yaml b/galaxy/templates/deployment-workflow.yaml index ee094f58..b994fbc9 100644 --- a/galaxy/templates/deployment-workflow.yaml +++ b/galaxy/templates/deployment-workflow.yaml @@ -1,3 +1,4 @@ +--- apiVersion: apps/v1 kind: Deployment metadata: diff --git a/galaxy/templates/hook-cvmfs-fix.yaml b/galaxy/templates/hook-cvmfs-fix.yaml index 1caa21ba..a954ae77 100644 --- a/galaxy/templates/hook-cvmfs-fix.yaml +++ b/galaxy/templates/hook-cvmfs-fix.yaml @@ -1,5 +1,6 @@ {{- if and .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} # Include the code you want to run when both conditions are met +--- apiVersion: batch/v1 kind: Job metadata: diff --git a/galaxy/templates/ingress-activity-canary.yaml b/galaxy/templates/ingress-activity-canary.yaml index 09c467e1..4cee4b9e 100644 --- a/galaxy/templates/ingress-activity-canary.yaml +++ b/galaxy/templates/ingress-activity-canary.yaml @@ -6,6 +6,7 @@ {{- $fullName := include "galaxy.fullname" . -}} {{- $ingressPath := .Values.ingress.path -}} {{- $servicePort := .Values.service.port -}} +--- apiVersion: networking.k8s.io/v1 kind: Ingress metadata: @@ -42,4 +43,4 @@ spec: number: {{ $servicePort }} {{- end }} {{- end }} ---- + diff --git a/galaxy/templates/ingress-tusd.yaml b/galaxy/templates/ingress-tusd.yaml index ebb836a9..36180356 100644 --- a/galaxy/templates/ingress-tusd.yaml +++ b/galaxy/templates/ingress-tusd.yaml @@ -1,5 +1,6 @@ {{- if and .Values.tusd.enabled .Values.tusd.ingress.enabled -}} {{- $fullName := include "galaxy.fullname" . -}} +--- apiVersion: networking.k8s.io/v1 kind: Ingress metadata: @@ -38,4 +39,4 @@ spec: {{- end }} {{- end }} {{- end }} ---- + diff --git a/galaxy/templates/ingress.yaml b/galaxy/templates/ingress.yaml index 9b2458e6..a77b9a2d 100644 --- a/galaxy/templates/ingress.yaml +++ b/galaxy/templates/ingress.yaml @@ -1,6 +1,7 @@ {{- if .Values.ingress.enabled -}} {{- $fullName := include "galaxy.fullname" . -}} {{- $servicePort := .Values.service.port -}} +--- apiVersion: networking.k8s.io/v1 kind: Ingress metadata: @@ -39,4 +40,3 @@ spec: {{- end }} {{- end }} {{- end }} ---- diff --git a/galaxy/templates/jobs-init.yaml b/galaxy/templates/jobs-init.yaml index d72244da..92079e07 100644 --- a/galaxy/templates/jobs-init.yaml +++ b/galaxy/templates/jobs-init.yaml @@ -1,3 +1,4 @@ +--- apiVersion: batch/v1 kind: Job metadata: diff --git a/galaxy/templates/priorityclass-job.yaml b/galaxy/templates/priorityclass-job.yaml index df518387..da4f9b59 100644 --- a/galaxy/templates/priorityclass-job.yaml +++ b/galaxy/templates/priorityclass-job.yaml @@ -1,4 +1,5 @@ {{- if and .Values.jobs.priorityClass.enabled (not .Values.jobs.priorityClass.existingClass) }} +--- apiVersion: scheduling.k8s.io/v1 kind: PriorityClass metadata: diff --git a/galaxy/templates/pv-s3fs.yaml b/galaxy/templates/pv-s3fs.yaml index 2948960c..4b0fb2fd 100644 --- a/galaxy/templates/pv-s3fs.yaml +++ b/galaxy/templates/pv-s3fs.yaml @@ -1,4 +1,5 @@ {{- if and .Values.refdata.enabled (eq .Values.refdata.type "s3csi") }} +--- apiVersion: v1 kind: PersistentVolume metadata: diff --git a/galaxy/templates/pvc-galaxy.yaml b/galaxy/templates/pvc-galaxy.yaml index c6426020..975f5c53 100644 --- a/galaxy/templates/pvc-galaxy.yaml +++ b/galaxy/templates/pvc-galaxy.yaml @@ -1,4 +1,5 @@ {{ if and .Values.persistence.enabled (not .Values.persistence.existingClaim) -}} +--- apiVersion: v1 kind: PersistentVolumeClaim metadata: @@ -23,4 +24,3 @@ spec: requests: storage: {{ .Values.persistence.size | quote }} {{ end }} ---- diff --git a/galaxy/templates/pvc-refdata.yaml b/galaxy/templates/pvc-refdata.yaml index a537eb03..a258f92b 100644 --- a/galaxy/templates/pvc-refdata.yaml +++ b/galaxy/templates/pvc-refdata.yaml @@ -1,4 +1,5 @@ {{- if .Values.refdata.enabled }} +--- apiVersion: v1 kind: PersistentVolumeClaim metadata: @@ -18,5 +19,4 @@ spec: {{- if eq $.Values.refdata.type "cvmfs" }} storageClassName: {{ tpl .Values.cvmfs.storageClassName . }} {{- end }} ---- {{- end }} diff --git a/galaxy/templates/rabbitmqcluster.yaml b/galaxy/templates/rabbitmqcluster.yaml index f215fc3b..1b100004 100644 --- a/galaxy/templates/rabbitmqcluster.yaml +++ b/galaxy/templates/rabbitmqcluster.yaml @@ -1,4 +1,5 @@ {{- if and .Values.rabbitmq.enabled (not .Values.rabbitmq.existingCluster) }} +--- apiVersion: rabbitmq.com/v1beta1 kind: RabbitmqCluster metadata: diff --git a/galaxy/templates/rbac-job.yaml b/galaxy/templates/rbac-job.yaml index f1180267..f80b5e1a 100644 --- a/galaxy/templates/rbac-job.yaml +++ b/galaxy/templates/rbac-job.yaml @@ -1,4 +1,5 @@ {{ if .Values.rbac.enabled }} +--- kind: Role apiVersion: rbac.authorization.k8s.io/v1 metadata: diff --git a/galaxy/templates/secret-galaxy.yaml b/galaxy/templates/secret-galaxy.yaml index 3ee42943..5c0ed980 100644 --- a/galaxy/templates/secret-galaxy.yaml +++ b/galaxy/templates/secret-galaxy.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 kind: Secret type: Opaque diff --git a/galaxy/templates/service-galaxy.yaml b/galaxy/templates/service-galaxy.yaml index 35fd5a1f..666dc20c 100644 --- a/galaxy/templates/service-galaxy.yaml +++ b/galaxy/templates/service-galaxy.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 kind: Service metadata: diff --git a/galaxy/templates/service-nginx.yaml b/galaxy/templates/service-nginx.yaml index 1b1e9f04..c2cef838 100644 --- a/galaxy/templates/service-nginx.yaml +++ b/galaxy/templates/service-nginx.yaml @@ -1,3 +1,4 @@ +--- apiVersion: v1 kind: Service metadata: diff --git a/galaxy/templates/service-tusd.yaml b/galaxy/templates/service-tusd.yaml index 0f4a7454..572848eb 100644 --- a/galaxy/templates/service-tusd.yaml +++ b/galaxy/templates/service-tusd.yaml @@ -1,4 +1,5 @@ {{ if .Values.tusd.enabled -}} +--- apiVersion: v1 kind: Service metadata: diff --git a/galaxy/templates/serviceaccount.yaml b/galaxy/templates/serviceaccount.yaml index 8560763e..435da946 100644 --- a/galaxy/templates/serviceaccount.yaml +++ b/galaxy/templates/serviceaccount.yaml @@ -1,4 +1,5 @@ {{- if .Values.serviceAccount.create -}} +--- apiVersion: v1 kind: ServiceAccount metadata: From 859c6b7c31949feab84c6c91acaf1d1f2838d30c Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Thu, 21 Mar 2024 12:41:53 -0400 Subject: [PATCH 18/25] 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 c36336d2b8a69ea0e2645f2a7194ae115adade4b Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 16 Apr 2024 20:55:46 +0000 Subject: [PATCH 19/25] Automatic Version Bumping from 5.9.0 to 5.10.0 --- galaxy/Chart.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml index 572b68bb..f446ec96 100644 --- a/galaxy/Chart.yaml +++ b/galaxy/Chart.yaml @@ -1,7 +1,7 @@ apiVersion: v2 name: galaxy type: application -version: 5.9.0 +version: 5.10.0 appVersion: "23.1" description: Chart for Galaxy, an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. icon: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png From e81042cdb9751bc70d8f75c368dd765164a26ba6 Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Tue, 16 Apr 2024 16:09:13 -0500 Subject: [PATCH 20/25] 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}}" From dfceb29c93dbd42d90cae0fdea103944fdd2f5ea Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Wed, 17 Apr 2024 11:09:28 -0400 Subject: [PATCH 21/25] Add checkout set to the tag-and-release step. --- .github/workflows/packaging.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml index 7436a068..e168fe5b 100644 --- a/.github/workflows/packaging.yml +++ b/.github/workflows/packaging.yml @@ -56,6 +56,9 @@ jobs: && contains(needs.*.result, 'success') && !contains(needs.*.result, 'failure') steps: + - uses: actions/checkout@v2 + with: + persist-credentials: false - name: Tag and release run: | version=v$(cat galaxy/Chart.yaml | grep ^version: | awk '{print $2}') From 7236270bd6c064e68e4374f54181969193dc80f8 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Wed, 17 Apr 2024 11:58:28 -0400 Subject: [PATCH 22/25] Update .github/workflows/packaging.yml Use latest version of the checkout action. Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> --- .github/workflows/packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml index e168fe5b..ae7191ac 100644 --- a/.github/workflows/packaging.yml +++ b/.github/workflows/packaging.yml @@ -56,7 +56,7 @@ jobs: && contains(needs.*.result, 'success') && !contains(needs.*.result, 'failure') steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: persist-credentials: false - name: Tag and release From 576807e64a0f9b1546fd5137d3a94df5468802f8 Mon Sep 17 00:00:00 2001 From: Keith Suderman Date: Wed, 17 Apr 2024 12:06:51 -0400 Subject: [PATCH 23/25] Update all checkout actions to v4 --- .github/workflows/packaging.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml index ae7191ac..a1bb5195 100644 --- a/.github/workflows/packaging.yml +++ b/.github/workflows/packaging.yml @@ -20,7 +20,7 @@ jobs: name: Package and push from PR runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: persist-credentials: false - uses: cloudve/helm-ci@master @@ -36,7 +36,7 @@ jobs: name: Package and push manual invocation runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: persist-credentials: false - uses: cloudve/helm-ci@master From 60a4ecc93dcbe79227e28de48a77a5268af60525 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 17 Apr 2024 18:44:59 +0000 Subject: [PATCH 24/25] Automatic Version Bumping from 5.10.0 to 5.10.1 --- galaxy/Chart.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml index f446ec96..04d48e48 100644 --- a/galaxy/Chart.yaml +++ b/galaxy/Chart.yaml @@ -1,7 +1,7 @@ apiVersion: v2 name: galaxy type: application -version: 5.10.0 +version: 5.10.1 appVersion: "23.1" description: Chart for Galaxy, an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. icon: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png From ba6afdd7928285d0c2bc2c3146ad4112a5e7ce65 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 17 Apr 2024 18:46:54 +0000 Subject: [PATCH 25/25] Automatic Version Bumping from 5.10.1 to 5.11.0 --- galaxy/Chart.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml index 04d48e48..aad942ce 100644 --- a/galaxy/Chart.yaml +++ b/galaxy/Chart.yaml @@ -1,7 +1,7 @@ apiVersion: v2 name: galaxy type: application -version: 5.10.1 +version: 5.11.0 appVersion: "23.1" description: Chart for Galaxy, an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. icon: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png