Learn more about sharing your modules with the GParc community.
GParc is a repository and community where users can share and discuss their own GenePattern modules. Unregistered users can search for and download modules. Registered GParc users can:
GenePattern is a powerful genomic analysis platform that provides access to tools for gene expression analysis, next-generation sequencing, proteomics, SNP analysis, and common data processing tasks. The GenePattern team has released hundreds of modules. However, GenePattern also provides a tool for you to create your own modules. GPARC gives you a place to share these with the rest of the GenePattern community. GenePattern is developed at the Broad Institute.
To contact the GenePattern development team, email firstname.lastname@example.org.
Once you have wrapped your code into a GenePattern module, there is some basic testing that you should do before uploading it to GParc.
Remember to include your test files (or a representative subset of your test files) in your module ZIP archive so other people can use them as example data. You can include test files as Support files when you create your module.
These are some of the basic QA testing practices for modules released by the GenePattern development team. If you would like assistance in formulating a test plan or if you run into problems you can't solve during testing, you can talk to fellow users on the GParc forum or contact the GenePattern development team for assistance.
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Your module documentation should contain at least:
Remember to spellcheck and proofread your documentation.
The GenePattern development team distributes all module documentation in PDF to avoid compatibility and security issues. Be aware that if you are using a Macintosh to PDF your doc, the links in the text will be unclickable. If you have a number of links in your doc, we recommend PDFing the document on a non-Macintosh platform.
Tags are terms or keywords that can be assigned to an object, like a module, to help describe it. Since GParc supports searching by tag, an accurate set of tags can help make your module more visible to the people who want or need it for their analyses. The GParc development team has created a list of common tags that will be presented as autocomplete options as you type, if the tag you want matches a tag already created. (Note that you may need to wait a moment for that option to be displayed, then select it from the dropdown menu.) This way, we can avoid having similar tags with spelling differences, such as "Alignment" and "alingment". Tags are case-insensitive, so if you enter "Sequencing" and the tag "sequencing" already exists, your tag will automatically be adjusted to match the existing tag.
We understand, however, that as GParc grows, the need for new tags will also grow. Please help us maintain consistency in the tags by keeping the following points in mind:
We appreciatate for your help with this.
Q: I tried to upload my module, but the submission failed. Why?
A: There are a number of common reasons for a module submission to GParc to fail, and we have listed these below. If these notes do not resolve your submission issue, contact the email@example.com team for assistance.
Q: Can I add images to my module description?
A: Yes - the module edit form uses CKEditor, a powerful rich-text editor with many features. To upload an image in the edit module form:
More information on using CKEditor can be found in the CKEditor User's Guide.
Q: I uploaded a new version of my module. Why does it show up as a separate entry with the same name instead of being a second version of my existing module?
A: Modules are identified by their LSID within the manifest file rather than by name; the version is the final part of the LSID. For two ZIP bundles to be recognized as different versions of the same module, the LSID must be identical all the way up to the version number. Editing your module on a different server, a reinstalled server, or working on a clone of your module are some of the common ways that the LSID could have changed.
If you encounter this scenario, we recommend deleting the new module from GParc and then changing its LSID to match the existing module (except for version) before re-uploading. We don't recommend deleting the older version as that may be in use on other GenePattern servers and the LSID change can cause confusion on those servers. Deleting a module will remove any comments that were specific to that version, however any HTML documentation for the module will remain on GParc in case anyone has downloaded and installed that module.