Merge pull request #135 from martenson/toolsumsa

UMSA - configure panel views, cleanup toolset

Author: martenson

files/galaxy-umsa.grid.cesnet.cz/all_tools.yml

@@ -0,0 +1,49 @@
+name: Tools
+type: generic
+id: all_tools
+items:
+- sections:
+  - upload_file
+  - collection_operations
+  - expression_tools
+- id: general_text_label
+  text: General Text Tools
+  type: label
+- sections:
+  - text_manipulation
+  - table_manipulation
+  - filter_and_sort
+  - convert
+  - convert_formats
+  - builtin_converters
+- id: stats_viz
+  text: Statistics and Visualization
+  type: label
+- sections:
+  - visualization
+  - statistics
+  - machine_learning
+- id: umsa_label
+  text: UMSA TOOLS
+  type: label
+- sections:
+  - recetox
+  - recetox_aplcms
+  - camera
+  - chemicaltoolbox
+  - isa_tools
+  - xcms
+  - secimtools
+  - metams
+  - w4m
+  - metfrag
+  - sirius
+  - mspurity
+  - openms
+  - matchms
+  - mfassignr
+  - qcxms
+  - pre_processing
+  - post_processing
+  - proteomics
+  - recetox_test

files/galaxy-umsa.grid.cesnet.cz/config/tool_conf.xml

@@ -0,0 +1,156 @@
+<?xml version='1.0' encoding='utf-8'?>
+<toolbox monitor="true">
+  <section id="upload_file" name="Upload Data">
+    <tool file="data_source/upload.xml" />
+  </section>
+  <!-- <section id="data_source_tools" name="External Data">
+    <tool file="data_source/ucsc_tablebrowser.xml" />
+    <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
+    <tool file="data_source/ncbi_datasets.xml" />
+    <tool file="data_source/ebi_sra.xml" />
+    <tool file="data_source/sra.xml" />
+    <tool file="data_source/microbial_import.xml" />
+    <tool file="data_source/biomart.xml" />
+    <tool file="data_source/cbi_rice_mart.xml" />
+    <tool file="data_source/gramene_mart.xml" />
+    <tool file="data_source/fly_modencode.xml" />
+    <tool file="data_source/intermine.xml" />
+    <tool file="data_source/flymine.xml" />
+    <tool file="data_source/modmine.xml" />
+    <tool file="data_source/mousemine.xml" />
+    <tool file="data_source/ratmine.xml" />
+    <tool file="data_source/yeastmine.xml" />
+    <tool file="data_source/metabolicmine.xml" />
+    <tool file="data_source/worm_modencode.xml" />
+    <tool file="data_source/wormbase.xml" />
+    <tool file="data_source/zebrafishmine.xml" />
+    <tool file="data_source/eupathdb.xml" />
+    <tool file="data_source/hbvar.xml" />
+  </section> -->
+  <section id="send_data" name="Send Data">
+    <tool file="data_export/send.xml" />
+    <!-- <tool file="data_export/export_remote.xml" /> -->
+  </section>
+  <section id="collection_operations" name="Collection Operations">
+    <tool file="${model_tools_path}/unzip_collection.xml" />
+    <tool file="${model_tools_path}/zip_collection.xml" />
+    <tool file="${model_tools_path}/filter_failed_collection.xml" />
+    <tool file="${model_tools_path}/filter_empty_collection.xml" />
+    <tool file="${model_tools_path}/filter_null.xml" />
+    <tool file="${model_tools_path}/flatten_collection.xml" />
+    <tool file="${model_tools_path}/merge_collection.xml" />
+    <tool file="${model_tools_path}/relabel_from_file.xml" />
+    <tool file="${model_tools_path}/filter_from_file.xml" />
+    <tool file="${model_tools_path}/sort_collection_list.xml" />
+    <tool file="${model_tools_path}/harmonize_two_collections_list.xml" />
+    <tool file="${model_tools_path}/cross_product_flat.xml" />
+    <tool file="${model_tools_path}/cross_product_nested.xml" />
+    <tool file="${model_tools_path}/tag_collection_from_file.xml" />
+    <tool file="${model_tools_path}/apply_rules.xml" />
+    <tool file="${model_tools_path}/build_list.xml" />
+    <tool file="${model_tools_path}/build_list_1.2.0.xml" />
+    <tool file="${model_tools_path}/extract_dataset.xml" />
+    <tool file="${model_tools_path}/duplicate_file_to_collection.xml" />
+  </section>
+  <section id="expression_tools" name="Expression Tools">
+    <tool file="expression_tools/parse_values_from_file.xml"/>
+  </section>
+  <label id="general_text_label" text="General Text Tools" />
+  <section id="text_manipulation" name="Text Manipulation">
+    <tool file="filters/fixedValueColumn.xml" />
+    <tool file="filters/catWrapper.xml" />
+    <tool file="filters/cutWrapper.xml" />
+    <tool file="filters/mergeCols.xml" hidden="true" />
+    <tool file="filters/convert_characters.xml" />
+    <tool file="filters/CreateInterval.xml" />
+    <tool file="filters/cutWrapper.xml" />
+    <tool file="filters/changeCase.xml" />
+    <tool file="filters/pasteWrapper.xml" />
+    <tool file="filters/remove_beginning.xml" />
+    <tool file="filters/randomlines.xml" />
+    <tool file="filters/headWrapper.xml" />
+    <tool file="filters/tailWrapper.xml" />
+    <tool file="filters/trimmer.xml" />
+    <tool file="filters/wc_gnu.xml" />
+    <tool file="filters/secure_hash_message_digest.xml" />
+  </section>
+  <section id="filter_and_sort" name="Filter and Sort">
+    <tool file="stats/filtering_1_1_0.xml" />
+    <tool file="stats/filtering.xml" />
+    <tool file="filters/sorter.xml" />
+    <tool file="filters/grep.xml" />
+    <tool file="filters/grep_1.0.1.xml"/>
+    <!-- <tool file="filters/gff/extract_GFF_Features.xml" />
+    <tool file="filters/gff/gff_filter_by_attribute.xml" />
+    <tool file="filters/gff/gff_filter_by_feature_count.xml" />
+    <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /> -->
+  </section>
+  <section id="table_manipulation" name="Table Manipulation">
+    <tool file="filters/joiner.xml" />
+    <tool file="filters/compare.xml" />
+    <tool file="stats/grouping.xml" />
+  </section>
+  <!-- <label id="genomic_manip_label" text="Genomic File Manipulation" />
+  <section id="convert_formats" name="Convert Formats">
+    <tool file="filters/axt_to_concat_fasta.xml" />
+    <tool file="filters/axt_to_fasta.xml" />
+    <tool file="filters/axt_to_lav.xml" />
+    <tool file="filters/bed2gff.xml" />
+    <tool file="filters/gff2bed.xml" />
+    <tool file="filters/lav_to_bed.xml" />
+    <tool file="maf/maf_to_bed.xml" />
+    <tool file="maf/maf_to_interval.xml" />
+    <tool file="maf/maf_to_fasta.xml" />
+    <tool file="filters/wiggle_to_simple.xml" />
+    <tool file="filters/sff_extractor.xml" />
+    <tool file="filters/gtf2bedgraph.xml" />
+    <tool file="filters/wig_to_bigwig.xml" />
+    <tool file="filters/bed_to_bigbed.xml" />
+    <tool file="extract/liftOver_wrapper.xml" />
+    <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
+    <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
+  </section> -->
+  <!-- <section id="fetch_sequences___alignments" name="Fetch Sequences / Alignments">
+    <tool file="maf/interval2maf_pairwise.xml" />
+    <tool file="maf/interval2maf.xml" />
+    <tool file="maf/maf_split_by_species.xml" />
+    <tool file="maf/interval_maf_to_merged_fasta.xml" />
+    <tool file="maf/genebed_maf_to_fasta.xml" />
+    <tool file="maf/maf_stats.xml" />
+    <tool file="maf/maf_thread_for_species.xml" />
+    <tool file="maf/maf_limit_to_species.xml" />
+    <tool file="maf/maf_limit_size.xml" />
+    <tool file="maf/maf_by_block_number.xml" />
+    <tool file="maf/maf_reverse_complement.xml" />
+    <tool file="maf/maf_filter.xml" />
+  </section> -->
+  <!-- <section id="mapping" name="Mapping" version="">
+    <tool file="sr_mapping/bfast_wrapper.xml" />
+    <tool file="sr_mapping/PerM.xml" />
+    <tool file="sr_mapping/srma_wrapper.xml" />
+    <tool file="sr_mapping/mosaik.xml" />
+  </section> -->
+  <!-- <section id="phenotype_association" name="Phenotype Association">
+    <tool file="phenotype_association/linkToGProfile.xml" />
+    <tool file="phenotype_association/linkToDavid.xml" />
+    <tool file="phenotype_association/ldtools.xml" />
+    <tool file="phenotype_association/pass.xml" />
+    <tool file="phenotype_association/gpass.xml" />
+    <tool file="phenotype_association/beam.xml" />
+    <tool file="phenotype_association/lps.xml" />
+    <tool file="phenotype_association/master2pg.xml" />
+  </section> -->
+  <section id="statistics" name="Statistics">
+    <tool file="stats/gsummary.xml" />
+    <tool file="filters/uniq.xml" />
+  </section>
+  <!-- <section id="motif_tools" name="Motif Tools">
+    <tool file="meme/meme.xml" hidden="True" />
+    <tool file="meme/fimo.xml" hidden="True" />
+  </section> -->
+  <section id="visualization" name="Visualization">
+    <tool file="plotting/bar_chart.xml" />
+    <tool file="plotting/boxplot.xml" />
+    <!-- <tool file="maf/vcf_to_maf_customtrack.xml" /> -->
+  </section>
+</toolbox>

files/usegalaxy.cz/all_tools.yml

@@ -18,6 +18,7 @@ items:
   - join__subtract_and_group
   - convert
   - convert_formats
+  - builtin_converters
 - id: genomic_manip_label
   text: Genomic File Manipulation
   type: label

galaxy.yml

@@ -215,7 +215,7 @@
         group: "{{ galaxy_user_group_name }}"
         mode: '0600'
       tags: cron
-      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz']"
+      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']"
       no_log: true
 
     - name: Copy user - group association script
@@ -243,7 +243,7 @@
         group: "{{ galaxy_user_group_name }}"
         mode: '0755'
       tags: cron
-      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz']"
+      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']"
     - name: Template tool installation cron script
       ansible.builtin.template:
         src: "{{ playbook_dir }}/templates/galaxy/cron/install_tools.sh.j2"
@@ -252,7 +252,7 @@
         group: "{{ galaxy_user_group_name }}"
         mode: '0755'
       tags: cron
-      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz']"
+      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']"
     - name: Schedule tool installation script using cron
       ansible.builtin.cron:
         name: "Install tool updates"
@@ -261,7 +261,7 @@
         hour: "3" # 3 am daily
         job: "/bin/bash -c 'URL={{ inventory_hostname }} API_KEY=$(cat /home/{{ galaxy_user_name }}/.galaxy_api_key) {{ galaxy_root }}/cron/tools/install_tools.sh 2>&1 | logger -t tool_install'"
       tags: cron
-      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz']"
+      when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']"
 
     - name: RE Galaxy instance patch in lib/galaxy/webapps/galaxy/api/job_files.py
       replace: