Static content for new assemblies: Difference between revisions

From Genecats
Jump to navigationJump to search
 
(7 intermediate revisions by 3 users not shown)
Line 8: Line 8:


===Browser tree:===
===Browser tree:===
Pushed from /usr/local/apache/htdocs/.….. from hgwdev to hgwbeta and the RR.
Pushed from /usr/local/apache/htdocs/.….. from hgwbeta to the RR/genome-euro.


====indexNews.html====
====goldenPath/newsarch.html====
# Save copy of most current announcement in another file: it will be entered into goldenPath/newsarch.html. 
# Copy an older new assembly announcement (find one on goldenPath/newsarch.html) to use as a template.
# Copy an older new assembly announcement (find one on goldenPath/newsarch.html) to use as a template.
# 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.
# Add it to the top of goldenPath/newsarch.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.
# 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.'''
# Add a new anchor (MMDDYY) for your announcement.
# Delete the oldest compressed announcement (at the bottom).
# Change the links to the credits page. There are two, each using a different anchor.  


====goldenPath/newsarch.html====
====indexNews.html====
# 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.
# Open the latest version of indexNews.html.
# Add a new anchor (MMDDYY)
# Use the instructions and template in the comment section at the top of the page to add a new entry.
# 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.
# Drop the last entry on the news list (there should be only 3 at a time).
# Be sure to check that your news item displays correctly on the home page. In particular make sure the headline does not exceed the max characters for the line, and check that you are consistent with style guidelines for date, caps, etc.
# Be sure the link goes to the appropriate spot added in goldenPath/newsarch.html (http://genome.ucsc.edu/goldenPath/newsarch.html#MMDDYY, where MMDDYY is the date found at the top of the announcement).


====goldenPath/credits.html====
====goldenPath/credits.html====
Line 40: Line 41:
# Copy the html from another organism and change the anchor, database references and the pairwise alignment section.
# Copy the html from another organism and change the anchor, database references and the pairwise alignment section.
# Add your organism to the pairwise alignment sections of any other organisms for which there are reciprocal chain/nets.
# Add your organism to the pairwise alignment sections of any other organisms for which there are reciprocal chain/nets.
# 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 http://hgwdev.cse.ucsc.edu/downloads.html ].
# 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.gi.ucsc.edu/downloads.html http://hgwdev.gi.ucsc.edu/downloads.html ]. BROKEN
# Note, starting in Oct. 2016 also add the assembly accession.version identifier: instead of (aptMan1) put (MPI-EVA AptMant0/[http://genome.ucsc.edu/cgi-bin/hgGateway?db=aptMan1 aptMan1])  (Full Data Set README and hgGateway have identifiers, see #18161).


===Kent Tree===
===Kent Tree===
====~/kent/src/hg/makeDb/trackDb/<org>/<assembly>/description.html====
====~/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)
# Test all searches to make sure are valid. Update or delete where necessary. Make sure a range query is included in the sample searches.  For instance (from hg18):
  RH18061;RH80175      Displays region between STS markers RH18061 and RH80175 or chromosome bands 15q11 to 15q13.
  15q11;15q13       This syntax may also be used for other range queries, such as between uniquely-determined   
                        ESTs, mRNAs, refSeqs, etc.
# Make sure the links, assembly info, and citations are valid and correctly formatted.
# Make sure the links, assembly info, and citations are valid and correctly formatted.
# Check spelling and grammar.
# Check spelling and grammar.
# If information seems lacking, check the makedoc, project site, or sponsor.
# 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
* Use the gbdbPush script to push the hgwdev /gbdb/ file from hgwdev to hgwbeta.
* Request a push of description.html from it's unique home at /gbdb/<org>/ (unlike htdocs static docs in apache) from hgwbeta to the RR like other gbdb files.  [http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_3_BETA_Steps#Beta:_Push_gbdb_files See gbdb examples].

Latest revision as of 16:53, 27 April 2020

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.

goldenPath/newsarch.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 goldenPath/newsarch.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. Add a new anchor (MMDDYY) for your announcement.
  4. Change the links to the credits page. There are two, each using a different anchor.

indexNews.html

  1. Open the latest version of indexNews.html.
  2. Use the instructions and template in the comment section at the top of the page to add a new entry.
  3. Drop the last entry on the news list (there should be only 3 at a time).
  4. Be sure to check that your news item displays correctly on the home page. In particular make sure the headline does not exceed the max characters for the line, and check that you are consistent with style guidelines for date, caps, etc.
  5. Be sure the link goes to the appropriate spot added in goldenPath/newsarch.html (http://genome.ucsc.edu/goldenPath/newsarch.html#MMDDYY, where MMDDYY is the date found at the top of the announcement).

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.gi.ucsc.edu/downloads.html . BROKEN
  6. Note, starting in Oct. 2016 also add the assembly accession.version identifier: instead of (aptMan1) put (MPI-EVA AptMant0/aptMan1) (Full Data Set README and hgGateway have identifiers, see #18161).

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
  • Use the gbdbPush script to push the hgwdev /gbdb/ file from hgwdev to hgwbeta.
  • Request a push of description.html from it's unique home at /gbdb/<org>/ (unlike htdocs static docs in apache) from hgwbeta to the RR like other gbdb files. See gbdb examples.
Retrieved from "https://genomewiki.ucsc.edu/genecats/index.php?title=Static_content_for_new_assemblies&oldid=5361"