Idea #8563
Updated by Sarah Guthrie about 8 years ago
Write a new wiki page describing: e.g., * Basic introduction to writing a Dockerfile (with links to more resources/references), resources/references?), using a small but real analysis tool * How to build your Docker image * How to upload your Docker image to Arvados * How to call your tool from a Crunch script, including best practices (using subprocess.Popen, capturing stdout, uploading results, setting success based on Popen's returncode) ** How to upload Ideally, include a few common output from the tool using arvados.crunch.TaskOutputDir() ** Explain when TaskOutputDir does not work: *** The tool writes things that fuse does not support (symbollic links and named pipes) *** The I/O access patterns are not performant with fuse (ex: 20 file handles on one file - tophat) ** For when it doesn't work, explain scenarios: how to use a tempdir and capture stdout; how to save one file from that directory or the as output; how to save an entire directory tree to Keep as output Some of this might be covered in the "Port a Pipeline" wiki page. If so, we might adapt some of its content.