Yannick Wurm

2-color cortex?

3

Hello, as discussed briefly with Zam, it would be pretty neat if cortex could handle two layers of colors: - one to identify sample as already exists - and one...

Are there reasons for/against: Bumping jQuery from 2.1.4 to 3.5 bumping clean-css from 3.4.28 to 4.1.11 bumping tester from 5.13 to 5.14.2 ?

(similarly to the ruby-side tests)

When more than 8? queries, should show a "next query" button

1

When many queries, we don't show an index (for obvious reasons). But it would still be handy to be able to navigate to next. "next" and "previous" buttons

Results page adaptive view breaking

1

Using Master on Safari (but not Brave) I currently get the index part on the left floating on top of the results https://www.loom.com/share/cf140623a2f441619da116df6eb3b50d

E.g, for tblastn, the "advanced parameters" field can take ` -db_gencode 4` (In order to change the genetic code) - but we don't show this in the help.

Downloads of HSP alignments - slight reformatting

3

- [ ] they should indicate a, b, c letters like so "-hit_1_hsp_c" (after the coordinate) - [ ] they should have whitespace (one newline) between HSPs

ruby versions - need to migrate support

8

So ruby 2.6.10 is no longer LTS supported (i.e. no more security updates). Some recent installs using ruby 3 have highlighted issues. Probably we will want to get everything to...

Sequence detection type failed (because its part AA part NT in this file - which should never exist in reality) and it returned `false`, but Seqserv tried to format the...

FASTA file detection is unreliable

3

In `makeblastdb.rb`, we use the following: ``` def probably_fasta?(file) File.read(file, 1) == '>' end ``` In rare cases, a file generated by makeblastdb begins with `>` despite not being a...