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 hgwbeta to the RR/genome-euro.

indexNews.html

1. Copy an older new assembly announcement (find one on goldenPath/newsarch.html) to use as a template.
2. Add it to the top of indexNews.html and 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.
3. Make sure the current announcements on indexNews.html have already been added to goldenPath/newsarch.html.
4. There should be commented-out compressed versions of the previous news announcements. Delete the oldest full announcement and uncomment its compressed version. 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.
5. Delete the oldest compressed announcement (at the bottom).
6. Create a compressed version of your announcement and comment it out.

goldenPath/newsarch.html

1. Copy your announcement from indexNews.html into newsarch.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) for your announcement.
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

• Edit in your hgdownload repository, be sure to do a "git pull" before starting to make changes.
• 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

1. Make sure the links, assembly info, and citations are valid and correctly formatted.
2. Check spelling and grammar.
3. If information seems lacking, check the makedoc, project site, or sponsor.

• make alpha on hgwdev in kent/src/hg/makeDb/trackDb/ copies description.html to /gbdb/<org>/html/description.html on hgwdev
• Request a push of description.html from it's unique home at /gbdb/<org>/ (unlike htdocs static docs in apache):

 Please push: /gbdb/<org>/html/description.html  from hgwdev to hgnfs1 

Once pushed to hgnfs1, description.html is visible on both hgwbeta and the RR