Issue with running automatically on multiple files due to (BUTTON)clinker screen

[ghoresh11]

Hello,

I wrote a script that would automatically take pairs of GBK files and run clinker on them, as I am comparing multiple gene-clusters to each other. My problem is that at the end of every clinker run I get this screen:

(BUTTON) clinker

   Instructions:
     * Drag cluster names to re-order clusters
     * Hover over a locus to reveal box and handles; drag box to move the locus, drag handles to resize it, double click to flip
     * Click genes to anchor the figure around them
     * Right click genes to edit their labels
     * Click cluster names and legend entries to rename them
     * Click legend circles to change gene colours
     * Right click legend entries to remove them and hide links
     * Click scale bar text to change its length
     * Tweak other options below!

   If you found clinker useful, please cite:
          clinker & clustermap.js: Automatic generation of gene cluster comparison figures
          Cameron L.M. Gilchrist, Yit-Heng Chooi
          Bioinformatics. doi: https://doi.org/10.1093/bioinformatics/btab007`

Therefore, I cannot run it automatically as clinker requires input from the user at the end of each run. Is there a way to solve this?

I am running clinker as a subprocess from python using the following command:

clinker first.gbk second.gbk -p out.html -j 2 -f

Many thanks Gal

[clb21565]

just pinging that I have the same issue. I guess let me know if you found a good solution, lol, I will too...

[clb21565]

Hey there. I fixed it for me by doing the described process here: https://github.com/gamcil/clinker/commit/b328fd9635b9ac81b4d6789b49bd8fdfc27985b2 basically, if you comment out the line opening the html plot the html plot, well, doesn't open automatically. I think its dependent on how you installed clinker if it has the updated .py or not.