Patch to fix NFS permission problems

Instructions.md

Installations instructions

PR #314 had the unfortunate side effect of breaking some tools with permission denied or file not found errors. This affects Helms chart versions 5.10.0 through 5.14.0. Until that PR is rolled back please add the above YAML snippet when installing Galaxy to Kubernetes with the Galaxy Helm chart.

1. Use curl to download the nfs-fix.yml file. If you copy/paste the nfs-fix.yml file be sure to do so from the raw view

curl -o nfs-fix.yml https://gist.githubusercontent.com/ksuderman/7147b41832ab9434a243fbe58141a7a4/raw/c29820b60de205b0ab55d9d1c92acdaffa3894bb/nfs-fix.yml

2. Include the nfs-fix.yml file as one of the --values files in the helm install command.

helm install galaxy -n galaxy galaxy/galaxy --values my-values.yml --values nfs-fix.yml

NOTE If you installed Galaxy using a different deployment name or installed Galaxy to a different namespacee you will have to adjust the above command accordingly.

nfs-fix.yml

configs:
  job_conf.yml:
    runners:
      k8s:
        k8s_data_volume_claim: null
        k8s_working_volume_claim: null
        k8s_persistent_volume_claims: |-
          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
          {{- if .Values.refdata.enabled -}}
          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org
          {{- end -}}
          {{- if .Values.setupJob.downloadToolConfs.enabled -}}
          ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}
          {{- end -}}
          {{- if .Values.extraVolumes -}}
          {{- template "galaxy.extra_pvc_mounts" . -}}
          {{- end }}