Update tools/snp50k/index.html with links to SNP50k markers on WM82.A6

[StevenCannon-USDA]

Added links to JBrowse WM82.A6

Problem -- flagging @nathanweeks or @ChenProm-USDA : I can't see how to update jekyll-theme-legumeinfo.
I have tried:

  git submodule update --remote _themes/jekyll-theme-legumeinfo
  git commit -m 'update theme submodule' _themes/jekyll-theme-legumeinfo

[nathanweeks]

In the "main" branch, it looks as though the _themes/jekyll-theme-legumeinfo git submodule already points to the latest commit in the legumeinfo/jekyll-theme-legumeinfo repo.

[StevenCannon-USDA]

In the "main" branch, it looks as though the _themes/jekyll-theme-legumeinfo git submodule already points to the latest commit in the legumeinfo/jekyll-theme-legumeinfo repo.

It may be that the problem is just on my end, and that the PR is fine as-is.

My understanding of submodules is lacking. Here is what I see with git diff _themes/jekyll-theme-legumeinfo:

diff --git a/_themes/jekyll-theme-legumeinfo b/_themes/jekyll-theme-legumeinfo
--- a/_themes/jekyll-theme-legumeinfo
+++ b/_themes/jekyll-theme-legumeinfo
@@ -1 +1 @@
-Subproject commit 51fdcb9f017b61f775c9f3e56b03e7bf4460cf96
+Subproject commit 51fdcb9f017b61f775c9f3e56b03e7bf4460cf96-dirty

How do I sync _themes/jekyll-theme-legumeinfo to the remote submodule's "main"? If I cd to _themes/jekyll-theme-legumeinfo, I get "HEAD detached".
The changes in the submodule, btw, are modified: assets/uikit (new commits)

[nathanweeks]

Are there any uncommitted changes in _themes/jekyll-theme-legumeinfo? What does git status show?

git submodule update --recursive from the superproject should recursively update the working tree of the submodules to reflect the commits that are pointed to by the superproject.

[StevenCannon-USDA]

@nathanweeks - I think I am back in business now. Earlier today I did this:

  git checkout --recurse
    cd _themes/jekyll-theme-legumeinfo/
    git checkout --recurse v1.3.0
    cd ../..

and now git status shows nothing to commit, working tree clean.

So, I think this is ready for review & merge, if the changes look OK.

[nathanweeks]

LGTM, though I'll proffer a Liquid loop to generate all rows for the table (feel free to use or not):

    {% assign assemblies = "1,2,4,6" | split: "," %}
    {% for assembly in assemblies %}
    <tr>
      <th><b>Wm82.a{{ assembly }}</b></th>
      {% for chromosome in (1..20) %}
      {% assign chr = chromosome | prepend: '00' | slice: -2,2 %}
      <td><a href="/assets/js/jbrowse/?assembly=Wm82.gnm{{ assembly }}&tracks=Wm82.gnm{{ assembly }}.ann1,Wm82.gnm{{ assembly }}.mrk.SoySNP50K&loc=glyma.Wm82.gnm{{ assembly }}.Gm{{ chr }}:1-1000000" target="_blank">Gm{{ chr }}</a></td>
      {% endfor %}
    </tr> 
    {% endfor %}

[StevenCannon-USDA]

... a Liquid loop to generate all rows for the table (feel free to use or not):

Thanks. I'll add that. I was also thinking that such a thing would be preferable.