Commit 692267e8 authored by Aaron Petkau's avatar Aaron Petkau

Removed importing workflow from toolshed because it does not work

parent 2fa7f6c4
......@@ -109,27 +109,7 @@ The core snp pipeline workflow is stored as a Galaxy workflow, which contains re
perl generate_galaxy_workflow.pl --local-toolshed localhost:9009/repos/aaron workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt > workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga
```
Please replace `localhost:9009/repos/aaron` with the location and user of the tools under your local toolshed. Once this Galaxy workflow file has been generated we can either directly upload the workflow to Galaxy instance or upload to a Galaxy tool shed using the below steps.
Upload Workflow to a Tool Shed
------------------------------
The workflow can be uploaded to a local Tool Shed and then installed to Galaxy using the following steps.
### Step 1: Upload Workflow to Tool Shed
1. Run the script `build_for_toolshed.sh`. This will generate a file `build/core_phylogenomics_pipeline_workflow.tar.gz` containing the workflow.
2. In the Galaxy Tool Shed, create a new repository to contain your workflow.
3. From the button at the top right that says **Upload files to repository** please upload the file containing the workflow `build/core_phylogenomics_pipeline_workflow.tar.gz`.
### Step 2: Install Workflow from Tool Shed to Galaxy
1. From the Galaxy instance go to **Admin** and then to **Search and browse tool sheds**.
2. Find the particular tool shed containing your workflow and then find the workflow repository you just uploaded.
3. Install this workflow into Galaxy.
4. Once the workflow is installed, you should be able to view the workflow from **Admin > Maange installed tool shed repositories**.
5. From here you should be able to view the workflow repository details. You should then be able to click on the workflow **Core SNP Pipeline** to view an image of this workflow.
6. Then, click on **Repository Actions** in the top right corner and there should be an option **Import workflow to Galaxy**.
Please replace `localhost:9009/repos/aaron` with the location and user of the tools under your local toolshed. Once this Galaxy workflow file has been generated we can directly upload the workflow to Galaxy instance using the below steps.
Upload Workflow Directly to a Galaxy Instance
---------------------------------------------
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment