Missing SVG Perl module

[sanger-pathogens]

Missing SVG Perl module

[satta]

Thanks Paolo for reporting this. To track this down I would like to ask if you installed the dependencies yourself (what distro and how did you install them) or used the Docker containers from Docker hub?

[pditommaso]

I should have mentioned. It is raised when using the Docker image satta/annot-nf. So, I think, something is missing there.

[satta]

Hmmm, I was using this myself on my Mac a while ago... strange. Will investigate, thanks.

[satta]

Should be fixed now with 0897b2e. Apparently the circos Debian package now does not list all of its dependencies...

[satta]

Docker hub images have been updated. You can try again if you want. The example completes for me:

[ss34@mib106184i:~/develop/annot-nf] ROOTDIR=`pwd` ../../nextflow -c loc_docker.config -c params_default.config run annot.nf -resume
N E X T F L O W  ~  version 0.14.1
Launching annot.nf
[warm up] executor > local
[00/7b6480] Cached process > contiguate_pseudochromosomes (1)
[ac/2585be] Cached process > press_ncRNA_cms (1)
...
[be/15b480] Submitted process > circos_run_chrs (1)
/Users/ss34/develop/annot-nf/work/tmp/20/d4bc5a0609b976ba50b88a7e0b3252/out.gaf
/Users/ss34/develop/annot-nf/work/be/15b48025d2971445cffd2c603ba5c6/image.png

[pditommaso]

Great! Not it works like a charm. BTW this is the biggest nextflow pipeline I have seen. Congrats.