Week Five | Advanced Galaxy tool development

Tasks

1. Work on Galaxy tool development Status: In progress Branch: None PR: None

2. Study Galaxy tool deployment Status: In progress Branch: None PR: None

3. Meeting with supervisors Status: Thursday Branch: None PR: None

Progress report

I’ve created a more advanced version of the netboxr Galaxy tool with more analysis and output options (commit) that I’ve tested using the data from the netboxr vignette for a better comparison. Unlike the prototype, the newest version accepts newline-delimited, as opposed to tab-delimited, files as input. Screenshots of the tool interface and output can be found below:

During our meeting this week @cannin pointed out that I when I originally made changes to the vignette to make it work without the cgdsr package (Issue 14), I introduced a bug where not all the required data (i.e. one table per gene) was used. I fixed this by uploading the four required tables in the inst folder, removing the “vignette_data.txt” file, and changing the code from:

dat <- read.table(system.file("vignette_data.txt", package = "netboxr"), header=TRUE, 
                                               sep="\t", stringsAsFactors=FALSE)

to:

dat <- read.table(system.file(paste("vignette_data_", gene, ".txt", sep = ""), package = "netboxr"), 
                                              header=TRUE, sep="\t", stringsAsFactors=FALSE)

This is the commit and the most recent GitHub Actions run for the above changes.

Changing intput to text (like cutoff value) Community detection method “lev” doesn’t work, figure out why Netboxr beta/alpha testing draft Try without virtual environment Change plotting parameters Iterations - help Fix number of genes, find out why Sink command How is it running, what is it doing Resolution not more than 1 Terminal output text file,