Merge pull request #3 from usegalaxy-eu/master

catching up

.github/requirements-python-lint.txt

@@ -0,0 +1,3 @@
+isort~=5.0
+flake8~=6.0
+flake8-docstrings~=1.0

.github/workflows/python.yml

@@ -8,11 +8,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-
-      - run: pip install --upgrade pip
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+          cache-dependency-path: '.github/requirements-python-lint.txt'
 
       - id: pip_install
-        run: pip install --upgrade isort~=5.0 flake8~=6.0 flake8-docstrings~=1.0
+        run: pip install -r '.github/requirements-python-lint.txt'
 
       - name: isort
         run: isort . --check --diff

.gitignore

@@ -34,3 +34,4 @@ dx_applets/.DS_Store
 #.gitignore
 #roles/*
 #*.code-workspace
+*.vscode/

beacon.yml

@@ -4,13 +4,25 @@
   hosts:
     - beacon
   vars_files:
-    - secret_group_vars/beacon.yml
+    - secret_group_vars/all.yml
+    - group_vars/all.yml
+    - group_vars/beacon/vars.yml
+    - group_vars/beacon/vault.yml
   vars:
-    postgres_data_dir: /data/postgresql/data
-    postgres_init_dir: /data/postgresql/init
-    bp_external_binding: 80
-    postgres_user: "{{ beacon_db_user }}"
-    postgres_pass: "{{ beacon_db_password }}"
-    postgres_external_binding: "{{ beacon_db_port }}"
+  collections:
+    - devsec.hardening
   roles:
+    - role: usegalaxy_eu.handy.os_setup
+      vars:
+        enable_hostname: true
+        enable_powertools: true        # geerlingguy.repo-epel role doesn't enable PowerTools repository
+        enable_remap_user: true
+        enable_create_user: true
+    - usegalaxy-eu.autoupdates  # keep all of our packages up to date
+    - influxdata.chrony
+    - dj-wasabi.telegraf
+    - usegalaxy-eu.dynmotd # nicer MOTD/welcome message
     - paprikant.beacon
+    - paprikant.beacon-importer
+#    - os_hardening
+#    - ssh_hardening

dokku.yml

@@ -126,6 +126,15 @@
         app: "{{ item }}"
       with_items: "{{ apps }}"
 
+    - name: Auto Renew Certs
+      ansible.builtin.cron:
+        name: Dokku Cert Autorenew
+        user: ubuntu
+        job: /usr/bin/dokku letsencrypt:auto-renew
+        hour: 4
+        minute: 59
+        # random values
+
     # - name: Clones
     #   dokku_clone:
     #     app: oembed

files/galaxy-test/tpv/interactive_tools.yml

@@ -124,6 +124,10 @@ tools:
     inherits: interactive_tool
     cores: 2
     mem: 8
+  interactive_tool_rstudio_askor:
+    inherits: interactive_tool
+    cores: 2
+    mem: 8
   interactive_tool_pyiron:
     inherits: interactive_tool
     cores: 1

files/galaxy-test/tpv/tools.yml

@@ -817,14 +817,5 @@ tools:
         - conda
 
   toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/.*:
-    cores: 8
-    mem: 56
-    rules:
-      - id: fragpipe_memory
-        if: |
-          parameters = {p.name: p.value for p in job.parameters}
-          parameters = tool.params_from_strings(parameters, app)
-          high_memory = parameters.get("high_memory", False)
-          high_memory
-        mem: 256
-        cores: 12
+    cores: 12
+    mem: 256

files/galaxy/config/email_domain_blocklist.conf

@@ -493,6 +493,7 @@ blogos.net
 blogspam.ro
 blondemorkin.com
 blow-job.nut.cc
+bltiwd.com
 bluedumpling.info
 bluewerks.com
 bnote.com
@@ -1452,6 +1453,7 @@ hazelnuts4u.com
 hazmatshipping.org
 hccmail.win
 headstrong.de
+healteas.com
 heathenhammer.com
 heathenhero.com
 hecat.es
@@ -1523,6 +1525,7 @@ i2pmail.org
 i6.cloudns.cc
 iaoss.com
 ibnuh.bz
+ibolinva.com
 icantbelieveineedtoexplainthisshit.com
 icemail.club
 ichigo.me
@@ -1699,6 +1702,7 @@ just-email.com
 justemail.ml
 juyouxi.com
 jwork.ru
+jxpomup.com
 kademen.com
 kadokawa.cf
 kadokawa.ga
@@ -1796,6 +1800,7 @@ kwift.net
 kwilco.net
 kyal.pl
 kyois.com
+kyrescu.com
 kzccv.com
 l-c-a.us
 l33r.eu
@@ -2601,9 +2606,11 @@ puttanamaiala.tk
 putthisinyourspamdatabase.com
 pwpwa.com
 pwrby.com
+qacmjeq.com
 qasti.com
 qbfree.us
 qc.to
+qejjyl.com
 qibl.at
 qiott.com
 qipmail.net
@@ -2860,6 +2867,7 @@ smellrear.com
 smellypotato.tk
 smtp99.com
 smwg.info
+smykwb.com
 snakebutt.com
 snakemail.com
 snapwet.com
@@ -3008,6 +3016,7 @@ stopspam.app
 storiqax.top
 storj99.com
 storj99.top
+stragedycd.com
 streetwisemail.com
 stromox.com
 stuckmail.com
@@ -3139,6 +3148,7 @@ thankyou2010.com
 thatim.info
 thejoker5.com
 thc.st
+the23app.com
 theaviors.com
 thebearshark.com
 thecarinformation.com
@@ -3564,6 +3574,7 @@ wuzupmail.net
 wwjmp.com
 wwwnew.eu
 wxnw.net
+wywnxa.com
 x24.com
 xagloo.co
 xagloo.com
@@ -3620,6 +3631,7 @@ yeezus.ru
 yep.it
 yermail.net
 yhg.biz
+yljthese.com
 ynmrealty.com
 yodx.ro
 yogamaven.com

files/galaxy/config/tool_data_table_conf.xml

@@ -196,4 +196,9 @@
         <columns>value, name, path, type</columns>
         <file path="/opt/galaxy/tool-data/ffindex_indices.loc" />
     </table>
+    <!-- huggingface models -->    
+    <table name="huggingface" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, pipeline_tag, domain, free_tag, version, path</columns>
+        <file path="/opt/galaxy/tool-data/huggingface.loc" />
+    </table>    
 </tables>

files/galaxy/config/user_preferences_extra_conf.yml

@@ -132,9 +132,8 @@ preferences:
                   # - ["Freiburg (Germany) - de.NBI cloud GPU - docker", remote_cluster_mq_docker_de03]
                   - ["Rennes (France) - GenOuest bioinformatics", fr-pulsar]
                   - ["Bari (Italy) - RECAS", it-pulsar]
-                  - ["Bari (Italy) - RECAS 2", it02-pulsar]
-                  # - ["Palermo (Italy) - GARR, 2wd true", remote_cluster_mq_2wdtrue_it03]
-                  # - ["Palermo (Italy) - GARR, 2wd falsef", remote_cluster_mq_2wdfalse_it03]
+                  - ["CINECA (Italy)", it02-pulsar]
+                  - ["GARR (Italy)", it03-pulsar]
                   # - ["Lisbon (Portugal) - Tecnico ULisboa", remote_cluster_mq_pt01]
                   # - ["Oxfordshire (UK) - Diamond Light Source", remote_cluster_mq_uk01]
                   # - ["Oxfordshire (UK) - Diamond Light Source - GPUs on docker", remote_cluster_mq_docker_uk01]
@@ -301,3 +300,11 @@ preferences:
               label: API Read Access Token
               type: password
               required: False
+
+    chatgpt:
+        description: Your OpenAI API key. This will be used for example for ChatGPT.
+        inputs:
+            - name: api_key
+              label: API Key
+              type: password
+              required: False