genomicsaotearoa / long-read-assembly Goto Github PK

Few different versions are available as modules

$ module spider Seqkit 
     Versions:
        SeqKit/0.15.0
        SeqKit/2.1.0
        SeqKit/2.2.0
        SeqKit/2.4.0

$ module load SeqKit/2.4.0

$ seqkit version
seqkit v2.4.0

ModDotPlot install

Merqury and meryl install - Might be easier to be included in the same module

There are additional files which are PDFs that need to be neatly embedded. Currently finding a method for it to work with Mkdocs.

Liftoff install and test https://github.com/agshumate/Liftoff

cutadapt install as a module

Add notes for instructors - mainly around symlinks, and backups

• This doesn't have to be part of the main docs/pages.

add gfastats as a module (latest version)

• Seqkit #8
• CutAdapt #11
• Nanocomp #13
• Best #5
• Verkko 1.3.1 #1
• Hifiasm (latest) #4
• Yak (latest) #9
• mashmap (including [generatedotplot] #7 (https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot))
• meryl #6
• Merqury (https://github.com/marbl/merqury) #6
• Winnowmap #3
• gfastats #10
• minimap2 & k8 (for asmgene) #12
• FCS #14
  • This tool is a bit odd, you don't really install it you just download the runner script. The runner script reads in arguments and decides which Docker command to run. (So the take home is that we just need to be able to run either Docker or Singularity)
• Liftoff #15
• ModDotPlot #16

MashMap module with generateDotPlot

FROM hprc repo TO GA repo

scheduled from Saturday, 01st July 13:00hrs NZT - Sunday,02nd July 13:00hrs NZT

Nanocomp install

This is referring to the script that spawns merqury2 in this section.

The error is quite extensive and is in the slurm error file in this path: /nesi/project/nesi02659/lra/users/jboe440/day3_assembly_qc/merqury/merqury2.37248577.err

The script that was run is here: /nesi/project/nesi02659/lra/users/jboe440/day3_assembly_qc/merqury/3.3-merqury_trio.sl

3.3-merqury_trio.sl was modified to increase runtime due to failure to complete the first time, but did not run to completion and was killed by OOM.

@DininduSenanayake Can you take a look at it?

Supplementary on Filesystem, symlinks and accessing individual workspace from Jupyter file explorer ( similar to what we have done with Summer school )

as per https://genomicsaotearoa.github.io/long-read-assembly/supplementary/supplementary_2/#symlinks-shortcuts

Add TOC to index.md

minimap2 with k8

Please update this to prevent potential version clashes.

Pull the image from upstream

Add snapshots on how to open Virtual Desktops and troubleshooting.

• Mainly for Bandage and IGV

https://github.com/GenomicsAotearoa/long-read-assembly/blob/fba215fa5d51321d18c57534a0ff69b10942abe5/docs/stylesheets/extra.css#L4C35-L4C35

Hi @DininduSenanayake ! I was wondering if it would be possible to change the color of hyperlinks in the text to stand out a little bit more? Sorry to be nitpicky, maybe my eyes are bad 😓 but I just missed a couple of the hyperlinks when reading through the text because the blue is dark enough to be close to the black, especially for shorter text (e.g., Meryl in the screenshot)

No worries if not, though!

edit: oh, bolding the links could also work, but maybe having the color change just a bit brighter to stand out would be easier css-wise? not sure....