feat: Added filter tools and new version of Clonal cluster plotting

.gitignore

@@ -160,3 +160,4 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+.codiumai

Dockerfile

@@ -6,14 +6,14 @@ ARG SERVER_DIR
 USER root
 
 RUN apt-get -qq update && \
-    apt-get install -y git pkg-config default-libmysqlclient-dev gcc
+    apt-get install -y git pkg-config default-libmysqlclient-dev gcc ca-certificates mercurial
 
 # Clone Pyclone-VI tools from GitHUb
 RUN git clone https://github.com/jCHENEBY/galaxy-tool-pyclone-vi.git /galaxy/server/tools/pyclone_vi
 RUN chown -R galaxy:galaxy /galaxy/server/tools/pyclone_vi
 
 # Clone Cellular prevalence graph tools from GitHub
-RUN git clone https://github.com/jCHENEBY/galaxy-tool-plot-cluster-prevalence.git /galaxy/server/tools/plot_clusters_prevalence
+RUN git clone --branch v1.2.3 https://github.com/jCHENEBY/galaxy-tool-plot-cluster-prevalence.git /galaxy/server/tools/plot_clusters_prevalence
 #COPY plot_clusters_prevalence /galaxy/server/tools/plot_clusters_prevalence/
 RUN chown -R galaxy:galaxy /galaxy/server/tools/plot_clusters_prevalence
 
@@ -27,6 +27,10 @@ RUN git clone https://github.com/jCHENEBY/galaxy-tool-export-cbioportal-image.gi
 #COPY export_cbioportal_image /galaxy/server/tools/export_cbioportal_image/
 RUN chown -R galaxy:galaxy /galaxy/server/tools/export_cbioportal_image
 
+# Clone Query tabular fro IUC
+RUN hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/query_tabular /galaxy/server/tools/query_tabular
+RUN chown -R galaxy:galaxy /galaxy/server/tools/query_tabular
+
 ## Copy pyclone_vi tool
 #COPY tools/pyclone_vi /galaxy/server/tools/pyclone_vi
 #RUN chown -R galaxy:galaxy /galaxy/server/tools/pyclone_vi

config/galaxy.yml

@@ -6,25 +6,25 @@ gravity:
 galaxy:
     builds_file_path: /galaxy/server/tool-data/shared/ucsc/builds.txt.sample
     container_resolvers_config_file: ''
-    data_dir: /galaxy/server/database
+    data_dir: /database
     data_manager_config_file: /galaxy/server/config/data_manager_conf.xml.sample
     datatypes_config_file: /galaxy/server/config/datatypes_conf.xml.sample
     dependency_resolvers_config_file: /galaxy/server/config/dependency_resolvers_conf.xml
     external_service_type_config_file: /galaxy/server/config/external_service_types_conf.xml.sample
-    #file_path: /galaxy/server/database/datasets
+#    file_path: /galaxy/server/database/datasets
     integrated_tool_panel_config: /galaxy/server/config/integrated_tool_panel.xml
     job_metrics_config_file: /galaxy/server/config/job_metrics_conf.xml
-    #job_working_directory: /galaxy/server/database/jobs
+#    job_working_directory: /galaxy/server/database/jobs
     migrated_tools_config: /galaxy/server/config/migrated_tools_conf.xml
-    openid_config_file: /galaxy/server/config/openid_conf.xml
+    openid_config_file: /galaxy/server/config/openid_conf.xml.sample
     shed_data_manager_config_file: /galaxy/server/config/shed_data_manager_conf.xml
     shed_tool_config_file: /galaxy/server/config/shed_tool_conf.xml
     shed_tool_data_table_config: /galaxy/server/config/shed_tool_data_table_conf.xml
     static_enabled: true
-    tool_config_file: /galaxy/server/config/tool_conf.xml.sample
-   # tool_data_path: /galaxy/server/database/tool_data
+    tool_config_file: /galaxy/server/config/tool_conf.xml
+#    tool_data_path: /galaxy/server/database/tool_data
     tool_data_table_config_path: /galaxy/server/config/tool_data_table_conf.xml.sample
-   # tool_dependency_dir: /galaxy/server/database/dependencies
+#    tool_dependency_dir: /galaxy/server/database/dependencies
     tool_sheds_config_file: /galaxy/server/config/tool_sheds_conf.xml.sample
     ucsc_build_sites: /galaxy/server/tool-data/shared/ucsc/ucsc_build_sites.txt.sample
-    visualization_plugins_directory: config/plugins/visualizations
+    visualization_plugins_directory: config/plugins/visualizations

config/tool_conf.xml

@@ -89,6 +89,7 @@
     <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" />
+    <tool file="query_tabular/query_tabular.xml" />
   </section>
   <section id="group" name="Join, Subtract and Group">
     <tool file="filters/joiner.xml" />