Static content for new assemblies

Static Doc changes for New and Updated Assemblies

After editing the docs for your assembly, test them in your sandbox (make user at the top of the browser tree) or on hgwdev (make alpha at the top of the browser tree). To test changes to description.html, do a make or a make alpha in kent/src/hg/makeDb/trackDb/ on hgwdev.

Feel free to run docs by Donna before sending them out - she has a great eye for grammar and punctuation.

Browser tree:

Pushed from /usr/local/apache/htdocs/.….. from hgwdev to hgwbeta and the RR.

indexNews.html

1. Save copy of most current announcement in another file: it will be entered into goldenPath/newsarch.html.
2. Copy an older new assembly announcement (find one on goldenPath/newsarch.html) to use as a template.
3. Edit as needed (technical details on gateway description page, interesting bits about organism from outside links or wikipedia). Don't forget to edits links and anchors so they reference your assembly.
4. Compress the previous news announcement and edit the Read-More link to go to: http://genome.ucsc.edu/goldenPath/newsarch.html#MMDDYY, where MMDDYY is the date found at the top of the announcement. Remember the date, as you will use to it to create an anchor in newsarch.html.
5. Delete the oldest compressed announcement (at the bottom).

goldenPath/newsarch.html

1. Add the old announcement taken from indexNews.html. Make sure to change the font header so that it is the same as everywhere else on the page.
2. Add a new anchor (MMDDYY)
3. Change the links to the credits page. There are two, each using a different anchor. You have to remove the /goldenPath/ part, since newsarch is *already* in goldenPath.

goldenPath/credits.html

1. If this is a new organism, add it to the list at the top and add a subsection in alphabetical order for your organism. Otherwise just expand the appropriate section.
2. Talk to the sponsor about who should be listed here. As far as the UCSC side, credit anybody whose name appears in the pushQ along with Donna if she helped review the docs.
3. Edit the two anchors to reflect your organism (<org>_credits and <org>_use).

FAQ/FAQreleases.html

1. Add or update with the new information. Should be able to extract information from credits page.

Downloads

Pushed from /usr/local/apache/htdocs-hgdownload/.….. on hgwdev to /usr/local/apache/htdocs/.….. on hgdownload.

downloads.html

• Pushed from hgwdev to hgdownload

1. If this is a new organism, add it to the list at the top. Note that the organisms are in alphabetical order. If your organism is in the 'Sequence Downloads Only' section, remove it.
2. Either create a new subsection if this is a new organism (alphabetical order) or add to the previous subsection if the organism is already listed.
3. Copy the html from another organism and change the anchor, database references and the pairwise alignment section.
4. Add your organism to the pairwise alignment sections of any other organisms for which there are reciprocal chain/nets.
5. Note that none of these links can be fully tested until all of the downloads files are present on the RR; however, you can test that the links go to the correct corresponding places on hgwdev from http://hgwdev.cse.ucsc.edu/downloads.html .

Kent Tree

~/kent/src/hg/makeDb/trackDb/<org>/<assembly>/description.html

• make alpha on hgwdev in kent/src/hg/makeDb/trackDb/ copies description.html to /gbdb/<org>/html/description.html on hgwdev
• /gbdb/<org>/html/description.html is pushed from hgwdev to hgnfs1 (where it is visible on both hgwbeta and the RR)

1. Test all searches to make sure are valid. Update or delete where necessary.
2. Make sure the links, assembly info, and citations are valid and correctly formatted.
3. Check spelling and grammar.
4. If information seems lacking, check the makedoc, project site, or sponsor.