Merge branch 'master' into grafana_update_version_11

usegalaxy-eu · Jul 23, 2024 · 4b8ecb6 · 4b8ecb6
2 parents 8eef755 + 0550b7b
commit 4b8ecb6
Show file tree

Hide file tree

Showing 27 changed files with 564 additions and 89 deletions.
diff --git a/.yamllint b/.yamllint
@@ -10,6 +10,7 @@ ignore: |
   files/galaxy/config
   files/galaxy-test/config
   files/galaxy-test/dynamic_rules/usegalaxy/
+  files/traefik/rules/template*
 
 rules:
   line-length: disable

diff --git a/files/galaxy/config/datatypes_conf.xml b/files/galaxy/config/datatypes_conf.xml
@@ -33,7 +33,7 @@
     <datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true"/>
     <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="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
+    <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"/>
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
       <converter file="bam_to_bai.xml" target_datatype="bai"/>
@@ -225,9 +225,9 @@
       <display file="igv/interval_as_bed.xml" inherit="true"/>
     </datatype>
     <datatype extension="jellyfish" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" description="Jellyfish database files are k-mer counts in binary format with a readable head. They are operated on and converted to human-readable text through jellyfish commands." />
-    <datatype extension="ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
-    <datatype extension="hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
-    <datatype extension="prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
+    <datatype extension="fastk_prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
     <datatype extension="npy" type="galaxy.datatypes.binary:Numpy" description="Standard format for saving numpy arrays" display_in_upload="true" description_url="https://numpy.org/devdocs/reference/generated/numpy.lib.format.html"/>
 
     <!-- ISA data types -->
@@ -395,6 +395,7 @@
     <datatype extension="star" type="galaxy.datatypes.images:Star" display_in_upload="true" />
     <datatype extension="peff" type="galaxy.datatypes.proteomics:PEFF" display_in_upload="true" />
     <datatype extension="toml" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
+    <datatype extension="colab.tar" auto_compressed_types="gz" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <!-- FlowCytometry -->
     <datatype extension="fcs" type="galaxy.datatypes.flow:FCS" mimetype="application/octet-stream" display_in_upload="true" description="A FCS binary sequence file with a '.fcs' file extension." />
@@ -949,10 +950,16 @@
     <!-- media datatypes -->
     <datatype extension="wav" type="galaxy.datatypes.media:Wav" display_in_upload="true" mimetype="audio/wav"/>
     <datatype extension="mp3" type="galaxy.datatypes.media:Mp3" display_in_upload="true" mimetype="audio/mp3"/>
+    <datatype extension="ogg" type="galaxy.datatypes.media:Ogg" display_in_upload="true" mimetype="audio/ogg"/>
+    <datatype extension="wma" type="galaxy.datatypes.media:Wma" display_in_upload="true" mimetype="audio/x-ms-wma"/>
     <datatype extension="mkv" type="galaxy.datatypes.media:Mkv" display_in_upload="true" mimetype="video/mkv"/>
     <datatype extension="mp4" type="galaxy.datatypes.media:Mp4" display_in_upload="true" mimetype="video/mp4"/>
     <datatype extension="flv" type="galaxy.datatypes.media:Flv" display_in_upload="true" mimetype="video/flv"/>
+    <datatype extension="webm" type="galaxy.datatypes.media:Webm" display_in_upload="true" mimetype="video/webm"/>
     <datatype extension="mpg" type="galaxy.datatypes.media:Mpg" display_in_upload="true" mimetype="video/mpeg"/>
+    <datatype extension="mov" type="galaxy.datatypes.media:Mov" display_in_upload="true" mimetype="video/quicktime"/>
+    <datatype extension="avi" type="galaxy.datatypes.media:Avi" display_in_upload="true" mimetype="video/x-msvideo"/>
+    <datatype extension="wmv" type="galaxy.datatypes.media:Wmv" display_in_upload="true" mimetype="video/x-ms-wmv"/>
     <!-- speech datatypes -->
     <datatype extension="textgrid" type="galaxy.datatypes.speech:TextGrid" display_in_upload="true" mimetype="text/plain"/>
     <datatype extension="par" type="galaxy.datatypes.speech:BPF" display_in_upload="true" mimetype="text/plain-bas"/>
@@ -1006,7 +1013,8 @@
     <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true" description="geospatial vector data format for geographic information system"/>
     <!-- Flexible Image Transport System (FITS) used in Astronomy https://fits.gsfc.nasa.gov/ https://fits.gsfc.nasa.gov/rfc4047.txt -->
     <datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
-    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true"/>
+    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/chain.html"/>
+    <datatype extension="ucsc.net" type="galaxy.datatypes.chain:Net" display_in_upload="true" description_url="https://genome.ucsc.edu/goldenPath/help/net.html"/>
   </registration>
   <sniffers>
     <!--
@@ -1102,7 +1110,7 @@
     <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
     <sniffer type="galaxy.datatypes.binary:Xlsx"/>
-    <sniffer type="galaxy.datatypes.binary:Numpy"/>    
+    <sniffer type="galaxy.datatypes.binary:Numpy"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
@@ -1111,6 +1119,7 @@
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.chain:Chain"/>
+    <sniffer type="galaxy.datatypes.chain:Net"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>
     <sniffer type="galaxy.datatypes.images:Gifti" />
@@ -1263,7 +1272,14 @@
     <sniffer type="galaxy.datatypes.media:Mp3"/>
     <sniffer type="galaxy.datatypes.media:Mp4"/>
     <sniffer type="galaxy.datatypes.media:Flv"/>
+    <sniffer type="galaxy.datatypes.media:Ogg"/>
     <sniffer type="galaxy.datatypes.media:Mpg"/>
+    <sniffer type="galaxy.datatypes.media:Mov"/>
+    <sniffer type="galaxy.datatypes.media:Avi"/>
+    <sniffer type="galaxy.datatypes.media:Wmv"/>
+    <sniffer type="galaxy.datatypes.media:Wma"/>
+    <sniffer type="galaxy.datatypes.media:Webm"/>
+    <sniffer type="galaxy.datatypes.media:Mkv"/>
     <sniffer type="galaxy.datatypes.speech:TextGrid" />
     <sniffer type="galaxy.datatypes.speech:BPF" />
     <sniffer type="galaxy.datatypes.larch:FEFFInput" />

diff --git a/files/galaxy/config/migrated_tools_conf.xml b/files/galaxy/config/migrated_tools_conf.xml
@@ -516,7 +516,8 @@
     </tool>
 </section>
 
-<section id="statistics" name="Statistics" version="">
+<!-- was never installed -->
+<!--section id="statistics" name="Statistics" version="">
   <tool file="toolshed.g2.bx.psu.edu/repos/devteam/dwt_var_perfeature/d56c5d2e1a29/dwt_var_perfeature/execute_dwt_var_perFeature.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/dwt_var_perfeature/dwt_var1/1.0.0">
       <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
         <repository_name>dwt_var_perfeature</repository_name>
@@ -525,7 +526,7 @@
         <id>toolshed.g2.bx.psu.edu/repos/devteam/dwt_var_perfeature/dwt_var1/1.0.0</id>
         <version>1.0.0</version>
     </tool>
-</section>
+</section-->
 
 <section id="rna_analysis" name="RNA-Seq" version="">
   <tool file="toolshed.g2.bx.psu.edu/repos/devteam/express/7b0708761d05/express/express_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/express/express/1.1.1">
@@ -692,7 +693,7 @@
     </tool>
 </section>
 
-<section id="variant_calling" name="Variant Calling">
+<!--section id="variant_calling" name="Variant Calling">
   <tool file="toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/33a0e6aca936/freebayes_wrapper/freebayes.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0">
       <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
         <repository_name>freebayes_wrapper</repository_name>
@@ -701,7 +702,7 @@
         <id>toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0</id>
         <version>0.5.0</version>
     </tool>
-</section>
+</section-->
 
 <section id="metagenomic_analyses" name="Metagenomic Analysis" version="">
   <tool file="toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/7b1b03c4465d/gi2taxonomy/gi2taxonomy.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0">

diff --git a/files/galaxy/tpv/destinations.yml.j2 b/files/galaxy/tpv/destinations.yml.j2
@@ -379,8 +379,8 @@ destinations:
   condor_singularity:
     inherits: basic_singularity_destination
     runner: condor
-    max_accepted_cores: 24
-    max_accepted_mem: 128
+    max_accepted_cores: 36
+    max_accepted_mem: 975
     min_accepted_gpus: 0
     max_accepted_gpus: 0
     params:

diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml
@@ -192,6 +192,9 @@ tools:
         - conda
         - singularity
 
+  toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/.*:
+    mem: 8
+
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/hifiasm_meta/hifiasm_meta/.*:
     cores: 8
     params:
@@ -213,6 +216,10 @@ tools:
     cores: 8
     mem: 8
 
+  ## a user exported 100 of files and memory was not enough
+  export_remote:
+    mem: 8
+
   toolshed.g2.bx.psu.edu/repos/rnateam/htseq-clip/htseq-clip/.*:
     cores: 4
     mem: 16
@@ -311,10 +318,17 @@ tools:
       require:
         - docker
 
+  toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/.*:
+    inherits: basic_docker_tool
   toolshed.g2.bx.psu.edu/repos/bgruening/mgnify_seqprep/mgnify_seqprep/.*:
     inherits: basic_docker_tool
+  toolshed.g2.bx.psu.edu/repos/artbio/manta/manta/.*:
+    inherits: basic_docker_tool
   toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy/squidpy_spatial/*:
     inherits: basic_docker_tool
+    mem: 6
+    env:
+      _GALAXY_JOB_TMP_DIR: '/tmp'
   toolshed.g2.bx.psu.edu/repos/goeckslab/gate_finder/gate_finder/.*:
     inherits: basic_docker_tool
   toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*:
@@ -1296,15 +1310,15 @@ tools:
         - singularity
 
   toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/.*:
+    inherits: basic_docker_tool
     cores: 8
-    mem: 40
+    mem: 42
+    env:
+      _GALAXY_JOB_TMP_DIR: '/tmp'
     rules:
       - id: funannotate_annotate_large_input
         if: input_size > 3.2
         mem: 62
-    scheduling:
-      require:
-        - singularity
 
   toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/.*:
     cores: 8
@@ -1318,9 +1332,9 @@ tools:
     cores: 12
     mem: 12
     env:
-      GENEMARK_PATH: /usr/local/tools/genemark/etp.for_braker/bin/
+      GENEMARK_PATH: /usr/local/tools/genemark/etp.for_braker/bin/gmes/
     params:
-      singularity_run_extra_arguments: "--env GENEMARK_PATH=/usr/local/tools/genemark/etp.for_braker/bin/"
+      singularity_run_extra_arguments: "--env GENEMARK_PATH=/usr/local/tools/genemark/etp.for_braker/bin/gmes/"
     scheduling:
       require:
         - singularity
@@ -1411,3 +1425,22 @@ tools:
 
   toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/.*:
     cores: 12
+
+  # Tool is same as fastqc so setting the same resources
+  toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/.*:
+    cores: 3
+
+  toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/Psortb/.*:
+    scheduling:
+      require:
+        - conda
+        - singularity
+
+  toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicinfo/hicexplorer_hicinfo/.*:
+    scheduling:
+      require:
+        - singularity
+
+  toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/.*:
+    cores: 8
+    mem: 56
diff --git a/files/traefik/rules/template-subdomains.yml b/files/traefik/rules/template-subdomains.yml
@@ -0,0 +1,54 @@
+{{define "subdomain"}}
+    prox-{{ . }}:
+      rule: HostRegexp(`^.+\\.{{ . }}\\.usegalaxy.eu`)
+      service: usegalaxy-eu
+      entryPoints:
+        - websecure
+      tls:
+        certResolver: "route53"
+        domains:
+          - main: "{{ . }}.usegalaxy.eu"
+            sans:
+              - "*.ep.interactivetool.{{ . }}.usegalaxy.eu"
+              - "*.{{ . }}.usegalaxy.eu"
+{{end}}
+
+http:
+  routers:
+{{template "subdomain" "assembly"}}
+{{template "subdomain" "nanopore"}}
+{{template "subdomain" "erasmusmc"}}
+{{template "subdomain" "climate"}}
+{{template "subdomain" "hicexplorer"}}
+{{template "subdomain" "annotation"}}
+{{template "subdomain" "metabolomics"}}
+{{template "subdomain" "metagenomics"}}
+{{template "subdomain" "microbiome"}}
+{{template "subdomain" "microgalaxy"}}
+{{template "subdomain" "rna"}}
+{{template "subdomain" "graphclust"}}
+{{template "subdomain" "ecology"}}
+{{template "subdomain" "proteomics"}}
+{{template "subdomain" "clipseq"}}
+{{template "subdomain" "cheminformatics"}}
+{{template "subdomain" "imaging"}}
+{{template "subdomain" "test"}}
+{{template "subdomain" "beta"}}
+{{template "subdomain" "streetscience"}}
+{{template "subdomain" "singlecell"}}
+{{template "subdomain" "humancellatlas"}}
+{{template "subdomain" "ml"}}
+{{template "subdomain" "live"}}
+{{template "subdomain" "plants"}}
+{{template "subdomain" "virology"}}
+{{template "subdomain" "lite"}}
+{{template "subdomain" "covid19"}}
+{{template "subdomain" "africa"}}
+{{template "subdomain" "india"}}
+{{template "subdomain" "spatialomics"}}
+{{template "subdomain" "materials"}}
+{{template "subdomain" "phage"}}
+{{template "subdomain" "earth-system"}}
+{{template "subdomain" "cancer"}}
+{{template "subdomain" "aqua"}}
+{{template "subdomain" "eirene"}}
diff --git a/files/traefik/rules/usegalaxy-eu-router.yml b/files/traefik/rules/usegalaxy-eu-router.yml
@@ -0,0 +1,13 @@
+http:
+  routers:
+    usegalaxy-eu-rtr:
+      rule: "Host(`usegalaxy.eu`) || HostRegexp(`^.+\\.usegalaxy\\.eu`)"
+      service: "usegalaxy-eu"
+      entryPoints:
+        - websecure
+      tls:
+        certResolver: "route53"
+        domains:
+          - main: "usegalaxy.eu"
+            sans:
+              - "*.ep.interactivetool.usegalaxy.eu"
diff --git a/files/traefik/rules/usegalaxy-eu-service.yml b/files/traefik/rules/usegalaxy-eu-service.yml
@@ -0,0 +1,10 @@
+http:
+  services:
+    usegalaxy-eu:
+      loadBalancer:
+        passHostHeader: true
+        sticky:
+          cookie: {}
+        servers:
+          - url: "https://sn06.galaxyproject.eu/"
+        #  - url: "https://sn07.galaxyproject.eu/"
diff --git a/group_vars/all.yml b/group_vars/all.yml
@@ -53,6 +53,9 @@ os_auditd_max_log_file_action: rotate
 os_auditd_space_left: 500
 os_auditd_space_left_action: suspend
 
+# Tailscale
+tailscale_args: "--accept-dns=false"
+
 # Telegraf
 telegraf_agent_package_state: latest
 telegraf_agent_output: