testing branch config

[colindaven]

Hi Sophia,

can you take a copy of this /ngsssd1/rcug/wochenende_test/CF_small elsewhere and test it with the config branches?

eg your .bashrc should look like this:

## Config for the metagenome analyzer Wochenende
export WOCHENENDE_DIR=/mnt/ngsnfs/tools/dev/we_config2/Wochenende
export HAYBALER_DIR=/mnt/ngsnfs/tools/dev/we_config2/haybaler
source /mnt/ngsnfs/tools/dev/we_config2/Wochenende/scripts/parse_yaml.sh
eval $(parse_yaml /mnt/ngsnfs/tools/dev/we_config2/Wochenende/config.yaml)

It's throwing can't find files errors in the haybaler section

thanks

[poer-sophia]

Is it this error?

Fatal error: cannot open file 'create_heattrees.R': No such file or directory

[poer-sophia]

Should be solved in config

[colindaven]

I updated the haybaler config branch

run_haybaler.sh was throwing - can't find pandas ....

[colindaven]

Instead of rerouting all output to /dev/null from Wochenende_postprocess.sh, do you think we should make a log ? Probably a good idea eh?

[poer-sophia]

Yeah that is a really good idea. I can't reproduc the pandas error... I even created the haybaler enviroment new from the env.yml because I thougth maybe I changed something with my enviroment but everything still works. I just started Wochenende and than postprocess from the config branch, I have no Idea why you get an error.

[colindaven]

Yeah, don't worry, the pandas error I fixed by loading the haybaler env in the script again. I don't generally expect the conda env to be required to be loaded when I start postprocess or run_haybaler.sh