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CAMI-challenge / CAMITAX

CAMITAX: Taxon labels for microbial genomes
https://doi.org/10.1101/532473
Apache License 2.0
29 stars 4 forks source link

Installation and running #18

Closed tenguzame closed 5 years ago

tenguzame commented 5 years ago

Dear Andreas, I'm trying to install your package, but it keeps throwing errors at me. Maybe there's something I got wrong in your installation procedures. First, I activated docker on my terminal and cloned this repository in my home. Then, I entered the new repository directory and installed nextflow using the command provided at their homepage ("curl -s https://get.nextflow.io | bash "). But when I enter your pull command, the program throws this error at me:

N E X T F L O W ~ version 19.01.0 ERROR ~ Project config file is malformed -- Cause: No signature of method: nextflow.config.ConfigParser$_parse_closure5.memory() is applicable for argument types: (String) values: [16 GB] Possible solutions: every(), every(), every(groovy.lang.Closure), every(groovy.lang.Closure), getAt(java.lang.String), getAt(java.lang.String)

I went to check for some typos in the nextflow.config file, and found that the program doesn't seem to like these lines: memory '24 GB' I tried to fix the typo by inserting all the required "="s and removed the ''s, but then, as I re-run the program, it throws the following error: ERROR ~ Project config file is malformed -- Cause: No signature of method: java.lang.Integer.call() is applicable for argument types: (ConfigObject) values: [[:]] What am I doing wrong? How should I install CAMITAX? Best regards

abremges commented 5 years ago

My mistake (and bad practice, sorry), should be fixed with https://github.com/CAMI-challenge/CAMITAX/commit/3ed20c16e0bce48791d26929ad311f1ce16ff1d6

I forgot to push the local config file after I committed a broken version to main. 👎 We are currently testing a new release candidate, should be online in 1-2 days... So either give it another try or wait for the tested version. Sorry again & thank you!

tenguzame commented 5 years ago

Dear Andreas, Thanks for the quick reply. I fixed the config file as you showed, but now nextflow complains it cannot pull anything because there are uncommitted changes. I guess I'll wait for your new release.

abremges commented 5 years ago

Possibly a side effect from cloning the repository first (which you don't need). Delete the cloned repository, then run nextflow drop CAMI-challenge/CAMITAX and nextflow pull CAMI-challenge/CAMITAX

But might be a good idea to wait a couple of days, the new release will also come with updated reference data = better results. I'll ask @AlphaSquad to also test it extensively in case I mess up things again. ;)

tenguzame commented 5 years ago

Well, then, I'll give it an immediate try to see if everything goes well, then I'll be using the updated version for the real thing. Thanks for your efforts!

abremges commented 5 years ago

Great, let me know if and how things work out! Notice that installation will take a while because 40 GB of reference data need to be downloaded first...

tenguzame commented 5 years ago

Managed to pull it yesterday evening! However, it throws me the following error, which prevents me from running it: WARN: There's no process matching config selector: centrifuge I checked everything but I can't see any error!

abremges commented 5 years ago

This is just a warning, no error, because there is no process centrifuge in init.nf (the database download). I'll try to find a better way but it should still run.

abremges commented 5 years ago

While the ugly warning is still in place, I just updated CAMITAX and confirmed that everything is working (for me). Please answer here or open a new issue if you run into trouble. Thanks!