restructure

Author: bgruening

Dockerfile

@@ -7,9 +7,9 @@ ENV GALAXY_CONFIG_BRAND GraphClust
 ENV ENABLE_TTS_INSTALL True
 
 # Install tools
-COPY  tools/graphclust_tools.yml $GALAXY_ROOT/tools.yaml
-COPY  tools/graphclust_tools2.yml $GALAXY_ROOT/tools_2.yaml
-COPY  tools/graphclust_utils.yml $GALAXY_ROOT/tools_3.yaml
+COPY  ./assets/tools/graphclust_tools.yml $GALAXY_ROOT/tools.yaml
+COPY  ./assets/tools/graphclust_tools2.yml $GALAXY_ROOT/tools_2.yaml
+COPY  ./assets/tools/graphclust_utils.yml $GALAXY_ROOT/tools_3.yaml
 
 RUN install-tools $GALAXY_ROOT/tools.yaml && \
     /tool_deps/_conda/bin/conda clean --tarballs --yes && \
@@ -28,7 +28,7 @@ RUN install-tools $GALAXY_ROOT/tools_3.yaml && \
 ADD ./tours/* $GALAXY_ROOT/config/plugins/tours/
 
 # Data libraries
-ADD ./assets/scrips/library_data.yaml $GALAXY_ROOT/library_data.yaml
+ADD ./assets/library/library_data.yaml $GALAXY_ROOT/library_data.yaml
 
 # Add workflows to the Docker image
 ADD ./workflows/*.ga $GALAXY_ROOT/workflows/
@@ -42,5 +42,5 @@ RUN startup_lite && \
     # setup-data-libraries -i $GALAXY_ROOT/library_data.yaml -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD
 
 # Container Style
-ADD ./img/workflow_early.png $GALAXY_CONFIG_DIR/web/welcome_image.png
+ADD ../assets/img/workflow_early.png $GALAXY_CONFIG_DIR/web/welcome_image.png
 ADD welcome.html $GALAXY_CONFIG_DIR/web/welcome.html

README.md

@@ -98,7 +98,7 @@ After running the Galaxy server, a web server is established under the host IP/U
 [This video tutorial](https://www.youtube.com/watch?v=fJ6tUt_6uas) can be helpful to get a visually comprehensive introduction on setting-up and running Galaxy-GraphClust.
 
 
-[![IMAGE ALT TEXT HERE](./img/video-thumbnail.png)](https://www.youtube.com/watch?v=fJ6tUt_6uas)
+[![IMAGE ALT TEXT HERE](./assets/img/video-thumbnail.png)](https://www.youtube.com/watch?v=fJ6tUt_6uas)
 
 ### Interactive tours
 Interactive Tours are available for Galaxy and Galaxy-GraphClust. To run the tours please on top panel go to **Help→Interactive Tours** and click on one of the tours prefixed **GraphClust workflow**. You can check the other tours for a more general introduction to the Galaxy interface.
@@ -119,7 +119,7 @@ GraphClust pipeline overview
 
 GraphClust pipeline for clustering similar RNA sequences together is a complex pipeline, for details please check GraphClust publication. Overall it consists of three major phases: a) sequence based pre-clustering b) encoding predicted RNA structures as graph features c) iterative fast candidate clustering then refinement
 
-![GraphClust pipeline overview (Heyne et al. 2012)](./img/graphclust_pipeline.png)
+![GraphClust pipeline overview (Heyne et al. 2012)](./assets/img/graphclust_pipeline.png)
 
 *GraphClust pipeline overview (Heyne et al. 2012)*