Merge branch 'master' into enable/gxadmin_galaxy_cleanup

Author: gsaudade99

.github/workflows/tpv.yml

@@ -26,6 +26,7 @@ jobs:
         run: |
           rm -f group_vars/htcondor/vault.yml
           rm -f group_vars/htcondor-secondary/vault.yml
+          rm -f group_vars/all/ssh-keys_vault.yml
 
       - name: Update git submodules.
         working-directory: "infrastructure-playbook"
@@ -177,6 +178,7 @@ jobs:
         run: |
           rm -f group_vars/htcondor/vault.yml
           rm -f group_vars/htcondor-secondary/vault.yml
+          rm -f group_vars/all/ssh-keys_vault.yml
 
       - name: Update git submodules.
         working-directory: "infrastructure-playbook"

files/galaxy/config/datatypes_conf.xml

@@ -34,6 +34,9 @@
     <datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true">
         <infer_from suffix="gfa" />
     </datatype>
+    <datatype extension="pnts" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" description="3D Tiles Point Cloud (PNTS) binary format for Cesium visualization" description_url="https://github.com/CesiumGS/3d-tiles/tree/main/specification/TileFormats/PointCloud">
+        <infer_from suffix="pnts" />
+    </datatype>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="A pairwise alignment format." description_url="https://genome.ucsc.edu/goldenPath/help/axt.html"/>

files/galaxy/tpv/destinations.yml.j2

@@ -126,6 +126,14 @@ destinations:
               else:
                   entity.params['submit_requirements'] = gpu_conditions
 
+  embedded_pulsar_docker_gpu_pxe_div4:
+    inherits: embedded_pulsar_docker_gpu_pxe
+    context:
+      galaxy_group: 'GalaxyGroup == "pxe-gpu-div4"'
+    scheduling:
+      require:
+        - pxe-gpu-div4
+
   #######################
   # PULSAR DESTINATIONS #
   #######################

files/galaxy/tpv/interactive_tools.yml

@@ -216,6 +216,9 @@ tools:
     mem: 8
     env:
       XLA_FLAGS: "--xla_gpu_cuda_data_dir=/op/conda/"
+    scheduling:
+      require:
+        - pxe-gpu-div4
 
   #interactive_tool_jupyter_notebook:
   #  inherits: interactive_tool

files/galaxy/tpv/tools.yml

@@ -532,7 +532,7 @@ tools:
       _GALAXY_JOB_TMP_DIR: '/tmp'
   toolshed.g2.bx.psu.edu/repos/bgruening/parabricks_fq2bam/parabricks_fq2bam/.*:
     inherits: basic_docker_tool
-    mem: 16
+    mem: 40
     gpus: 1
     cores: 16
     params:

files/galaxy/tpv/users.yml

@@ -8,7 +8,6 @@ users:
           'interactive_tool_jupyter_notebook' in tool.id
         cores: 1
         mem: 15
-  [email protected]:
   [email protected]:
     rules:
       - id: user-specific-notebook

traefik-proxy.yml

@@ -38,8 +38,6 @@
         - docker
         - selinux
 
-
-
     - name: Copy Galaxy active users script
       ansible.builtin.copy:
         src: files/traefik/active_users.sh