Name	Name	Last commit message	Last commit date
Latest commit chrishah automatically use uniprot that funannotate setup downloaded as physic… Aug 3, 2022 99061a0 · Aug 3, 2022 History 172 Commits
bin	bin	update	Aug 2, 2022
data	data	add gsc1 clusterfile	Aug 3, 2022
log	log	Fix small bug in eggnogdb setup. Add log dir.	Sep 7, 2020
notes	notes	some notes on how to run things	May 18, 2022
rules	rules	automatically use uniprot that funannotate setup downloaded as physic…	Aug 3, 2022
.gitignore	.gitignore	add some usage notes and cluster-config and config.yaml as template	Oct 15, 2020
HOWTO.setup	HOWTO.setup	update	Aug 3, 2022
Notes.md	Notes.md	add some usage notes and cluster-config and config.yaml as template	Oct 15, 2020
README.md	README.md	Update README	Jun 30, 2020
Snakefile	Snakefile	Add functional annotations for MAKER only predictions (annocomba -m m…	Nov 19, 2020
Snakefile_CH	Snakefile_CH	add rules, scripts, configs	Jun 16, 2020
TODO.md	TODO.md	Add some todos	Nov 10, 2020
annocomba	annocomba	fix eggnog path	Aug 3, 2022
rulegraph.pdf	rulegraph.pdf	Add rulegraph for whole pipeline	Aug 17, 2020
rulegraph.png	rulegraph.png	Add rulegraph for whole pipeline	Aug 17, 2020
setup.Snakefile	setup.Snakefile	Move setup parts to new snakefile	Oct 16, 2020

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A flexible genome annotation pipeline combining funannotate and MAKER, snakemake and singularity

Sauron: There is a strange issue with RepeatMasker. For some reason it does not run. ReapearMasking with TanTan works fine.
Sauron: I have had many jobs failing due to a singularity error: FATAL: container creation failed: failed to resolved session directory. This does not occur on VSC. From the extended message: Activating singularity image /cl_tmp/reslph/projects/xylographa_fun/.snakemake/singularity/195cc8bdbe1d3f304062822f8f4f06ce.simg FATAL: container creation failed: failed to resolved session directory /usertmp/singularity/mnt/session: lstat /tmp/singularity: no such file or directory I assume it has to do with the tmp directory not being present. I have seen this after the jobs have been in the queue for a week (and other jobs ran fine). Maybe the /tmp directory is automatically deleted from time to time which causes this error.

$ git clone [email protected]:reslp/annocomba.git
$ ./annocomba --setup