The Peanut Genome page - Githubissues

PeanutBase / jekyll-peanutbase

A "starter" Jekyll site that uses the jekyll-theme-legumeinfo submodule

Apache License 2.0

0 stars 0 forks source link

The Peanut Genome page #28

Closed svengato closed 1 year ago

svengato commented 1 year ago

The Peanut Genome https://dev.peanutbase.org/genome

Changes between genome assemblies v1 and v2 https://dev.peanutbase.org/genome/peanut_genome_v1_v2

Issues:

[ ] 1. Some links (IPGI, "Two diploid progenitors of cultivated peanut", GBrowse, JBrowse, data store assembly & annotation) still refer to the current peanutbase.org. Do we need to update these?
[ ] 2. "IMPORTANT NOTE: the version 2.0 assembly (gnm2) for Arachis hypogaea var. Tifrunner has not been submitted to GenBank." Is this still true?
[x] 3. Links to Aiden Lab and DNA Zoo Announcement are missing/obsolete, let me know if alternatives exist.
[x] 4. Dot plots: should these go in the repository? (no, on falafel)

svengato commented 1 year ago

Links to Aiden Lab and DNA Zoo Announcement are missing/obsolete, let me know if alternatives exist.

These are now fixed.

sdash-github commented 1 year ago

Some links (IPGI, "Two diploid progenitors of cultivated peanut", GBrowse, JBrowse, data store assembly & annotation) still refer to the current peanutbase.org. Do we need to update these?

YES

Dot plots: should these go in the repository?

We should keep them in falafel where PB files are stored and linked to. Only the page should go to pb-jekyll repo.

svengato commented 1 year ago

I moved the dot plots to falafel.

svengato commented 1 year ago

On the "Changes between v1 and v2" page, the Downloads links go to an old Legume Federation version of the data store. Should they go to the current LIS data store instead? And should we add the new gnm2.ann2 genome?

@sdash-github and @adf-ncgr : Should we link to the current data store, or leave it as is?

svengato commented 1 year ago

I made an IPGI (International Peanut Genome Initiative) page (under The Peanut Genome), but its content is pretty old and needs updating.

svengato commented 1 year ago

What is the correct format for phrases like "Arachis hypogaea var. Tifrunner"? I think the botanical name should be in italics, and the cultivar name should have no highlighting? There is some inconsistency across pages.

svengato commented 1 year ago

Initial commit: c30b6c4. This includes IPGI and Changes between genome assemblies v1 and v2 pages as well as the main page.

Known issues for main page (genome/index.html):

[x] Fix various links (v1 and v2 assembly, annotation, GBrowse, JBrowse).
[x] Fix link to "two diploid progenitors of cultivated peanut".
[x] Fix links to PeanutBase datastore - should they link to the LIS datastore?
[x] "IMPORTANT NOTE: the version 2.0 assembly (gnm2) for Arachis hypogaea var. Tifrunner has not been submitted to GenBank." Is this still true?

sdash-github commented 1 year ago

Genome page links rectified. To 'legacy.PB' and to correct DS link 'data.legumeinfo.org/Arachis' instead of 'PB/data/v2/etc.'
Commit: 6171e33

sdash-github commented 1 year ago

The pb-jekyll-site/genome page is ready. Any other refinement when needed will be done after transition. Closing issue.