Commit 61ec80ee authored by Aaron Petkau's avatar Aaron Petkau

Fixed up some of the documentation

parent df1b84fd
......@@ -111,13 +111,15 @@ Once the tools are installed the workflow under `workflows/` can be installed.
Step 1: Generating a Galaxy workflow file
-----------------------------------------
The core snp pipeline workflow is stored as a Galaxy workflow, which contains references to all tools used + tool sheds used to install these tools. For example freebayes is refered to as `galaxy-shed.corefacility.ca/repos/phil/freebayes/freebayes/0.0.4`. If you have installed any of the local tools in a differently named tool shed, than this full path will not work. To work around this issue, a template file is included for the workflow `workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt`. We can generate the Galaxy-usable workflow file from this template file b y using a command similar to:
The core snp pipeline workflow is stored as a Galaxy workflow, which contains references to all tools used + tool sheds used to install these tools. For example freebayes is refered to as `galaxy-shed.corefacility.ca/repos/phil/freebayes/freebayes/0.0.4`. If you have installed any of the local tools in a differently named tool shed, than this full path will not work. To work around this issue, a template file is included for the workflow `workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt`. We can generate the Galaxy-usable workflow file from this template file by using a command similar to:
```bash
$ 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
```
Step 1: Upload Workflow to Tool Shed
Once this Galaxy workflow file has been generated we directly upload to Galaxy instance or a Galaxy tool shed using the below steps.
Step 2: Upload Workflow to Tool Shed
------------------------------------
The workflow can be uploaded to a Galaxy Tool Shed using the following commands.
......@@ -126,7 +128,7 @@ The workflow can be uploaded to a Galaxy Tool Shed using the following commands
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
Step 3: Install Workflow from Tool Shed to Galaxy
-------------------------------------------------
To install a workflow from the Tool Shed into a running Galaxy instance please use the following steps.
......@@ -138,7 +140,7 @@ To install a workflow from the Tool Shed into a running Galaxy instance please u
Updating Workflow
=================
The pipeline workflow is stored as a Galaxy workflow, which contains references to all tools used + tool sheds used to install these tools. For example freebayes is refered to as `galaxy-shed.corefacility.ca/repos/phil/freebayes/freebayes/0.0.4`. If you have installed any of the local tools in a differently named tool shed, than this full path will not work. A template file is also included for the workflow `workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt`. If you wish to update the workflow, the template file can be generated with a command like:
If you wish to update the workflow, the template file can be generated with a command like:
```bash
sed -e 's/"[^"]*core_pipeline/"[% LOCAL_REPOSITORY %]\/core_pipeline/' -e 's/"[^"]*smalt_collection/"[% LOCAL_REPOSITORY %]\/smalt_collection/' -e 's/"[^"]*phyml/"[% LOCAL_REPOSITORY %]\/phyml/' -e 's/"[^"]*freebayes/"[% LOCAL_REPOSITORY %]\/freebayes/' path/to/Galaxy-Workflow-Core_SNP_Pipeline.ga > workflows/core_phylogenomics_pipeline_workflow/Galaxy-Workflow-Core_SNP_Pipeline.ga.tt
......
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