https://wiki.biocomputeobject.org/index.php?action=history&feed=atom&title=Galaxy_Workflow_Converter 2026-04-29T00:45:12Z Revision history for this page on the wiki MediaWiki 1.38.2 https://wiki.biocomputeobject.org/index.php?title=Galaxy_Workflow_Converter&diff=1309&oldid=prev 2026-04-14T21:38:47Z

<p>Created page with &quot;Workflows can be directly downloaded from Galaxy but file conversion is needed in order to transfer into BCODB successfully. Please follow the following steps to convert the file and validation: == File conversion == # Download the converter [https://github.com/FDA-ARGOS/data.argosdb/blob/main/lib/galaxy%20converter.py script] from GitHub. # On the local terminal, run the following command &lt;code&gt;python [converter script&#039;s name.py] -b [path to the file that needs to be co...&quot;</p> <p><b>New page</b></p><div>Workflows can be directly downloaded from Galaxy but file conversion is needed in order to transfer into BCODB successfully. Please follow the following steps to convert the file and validation:<br /> == File conversion ==<br /> # Download the converter [https://github.com/FDA-ARGOS/data.argosdb/blob/main/lib/galaxy%20converter.py script] from GitHub.<br /> # On the local terminal, run the following command &lt;code&gt;python [converter script's name.py] -b [path to the file that needs to be converted] -o [path to the output file]&lt;/code&gt;<br /> <br /> == Validation ==<br /> # Install Validation Package:<br /> ## On the local terminal, clone the repository first by &lt;code&gt;git clone https://github.com/biocompute-objects/bcotool&lt;/code&gt;<br /> ## Change directory: &lt;code&gt;cd bcotool/&lt;/code&gt;<br /> ## Go to virtual environment: &lt;code&gt;python -m venv env&lt;/code&gt;<br /> ## Activate virtual environment: &lt;code&gt;. env/bin/activate&lt;/code&gt;<br /> ## Install required packages: &lt;code&gt;pip install -r requirements.txt&lt;/code&gt;<br /> ## Run validation: &lt;code&gt;python bcotool/bco_runner.py validate -b [path to the converted file]&lt;/code&gt; (Note: if only run &lt;code&gt;python bcotool/bco_runner.py&lt;/code&gt;, more options can be seen.) If passed validation should show as the figure below [[File:Screen Shot 2022-11-09 at 16.38.10.png|800px|thumb|center]]<br /> ## If they encountered errors, will show as the figure below: [[File:Screen Shot 2022-11-09 at 16.46.07.png|800px|thumb|center]]<br /> ##* Open error log for error description: &lt;code&gt;open error.log&lt;/code&gt;<br /> <br /> == Upload ==<br /> # Converted JSON file can be uploaded to BCODB through copy/pasting the RAW JSON file directly on BCO Builder or through API, refer to API documentation [[BCO Portal Local Deployment|here]].</div>

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