Merge branch 'master' into galaxy_job_radar

usegalaxy-eu · Feb 28, 2025 · ecd41f8 · ecd41f8
2 parents 34c2721 + 51fda11
commit ecd41f8
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Showing 3 changed files with 23 additions and 8 deletions.
diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml
@@ -983,7 +983,7 @@ tools:
     mem: 90
     params:
       docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
-      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
+      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb09/galaxy_db/:rw,/data/dnb10/galaxy_db/:rw,/data/dnb11/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
       docker_default_container_id: centos:8.3.2011
     scheduling:
       require:
@@ -996,7 +996,7 @@ tools:
     mem: 20
     params:
       docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
-      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
+      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb09/galaxy_db/:rw,/data/dnb10/galaxy_db/:rw,/data/dnb11/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
       docker_default_container_id: centos:8.3.2011
     scheduling:
       require:
@@ -1007,7 +1007,7 @@ tools:
   '.*bioext_bam2msa.*':
     params:
       docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
-      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
+      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb09/galaxy_db/:rw,/data/dnb10/galaxy_db/:rw,/data/dnb11/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
       docker_default_container_id: centos:8.3.2011
     scheduling:
       require:
@@ -1017,7 +1017,7 @@ tools:
   'last_*':
     params:
       docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
-      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
+      docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb09/galaxy_db/:rw,/data/dnb10/galaxy_db/:rw,/data/dnb11/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
       docker_default_container_id: centos:8.3.2011
     scheduling:
       require:

diff --git a/group_vars/sn06/toolmsg.yml b/group_vars/sn06/toolmsg.yml
@@ -42,3 +42,18 @@ toolmsg_messages:
       <a href="https://usegalaxy.eu/?tool_id=bg_diamond">Diamond</a>
       instead. Pairwise alignment of proteins and translated DNA can be up to 100x-10,000x faster than BLAST.</strong>
     class: warning
+  - tool_id: toolshed.g2.bx.psu.edu/repos/maciek/spamr_vet_tools/mlst_amr_staramr
+    message: >
+      <strong>The <a href="https://toolshed.g2.bx.psu.edu/repository/view_repository?id=597eedd2a8e1f88b">SPAMR-VET tools</a>
+      are in-development tools currently offered for testing purposes only.</strong>
+    class: warning
+  - tool_id: toolshed.g2.bx.psu.edu/repos/maciek/spamr_vet_tools/quality_script_fastp_bracken
+    message: >
+      <strong>The <a href="https://toolshed.g2.bx.psu.edu/repository/view_repository?id=597eedd2a8e1f88b">SPAMR-VET tools</a>
+      are in-development tools currently offered for testing purposes only.</strong>
+    class: warning
+  - tool_id: toolshed.g2.bx.psu.edu/repos/maciek/spamr_vet_tools/quast_get_fasta
+    message: >
+      <strong>The <a href="https://toolshed.g2.bx.psu.edu/repository/view_repository?id=597eedd2a8e1f88b">SPAMR-VET tools</a>
+      are in-development tools currently offered for testing purposes only.</strong>
+    class: warning
diff --git a/templates/galaxy/config/object_store_conf.xml.j2 b/templates/galaxy/config/object_store_conf.xml.j2
@@ -198,7 +198,7 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no
             <files_dir path="/data/dnb09/galaxy_db/files"/>
             <extra_dir type="job_work" path="/data/jwd04/main"/>
         </backend>
-        <backend id="files27" type="disk" weight="0" store_by="uuid">
+        <backend id="files27" type="disk" weight="4" store_by="uuid">
             <badges>
                 <more_stable />
                 <!--backed_up></backed_up-->
@@ -211,21 +211,21 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no
             <files_dir path="/data/dnb10/galaxy_db/files"/>
             <extra_dir type="job_work" path="/data/jwd02f/main"/>
         </backend>
-        <backend id="files28" type="disk" weight="0" store_by="uuid">
+        <backend id="files28" type="disk" weight="4" store_by="uuid">
             <badges>
                 <more_stable />
             </badges>
             <files_dir path="/data/dnb10/galaxy_db/files"/>
             <extra_dir type="job_work" path="/data/jwd05e/main"/>
         </backend>
-        <backend id="files29" type="disk" weight="2" store_by="uuid">
+        <backend id="files29" type="disk" weight="1" store_by="uuid">
             <badges>
                 <more_stable />
             </badges>
             <files_dir path="/data/dnb11/galaxy_db/files"/>
             <extra_dir type="job_work" path="/data/jwd02f/main"/>
         </backend>
-        <backend id="files30" type="disk" weight="2" store_by="uuid">
+        <backend id="files30" type="disk" weight="1" store_by="uuid">
             <badges>
                 <more_stable />
             </badges>