CollectMultipleMetrics: there is no package called ‘tidyverse’ about grenepipe HOT 6 CLOSED

Hi Ben,

thanks for reporting this issue, that is indeed a funny one. I did not know that picard internally calls R scripts. Modern software... conda calling python calling snakemake calling python calling java calling R - no wonder that this is so fragile!

Anyway, should be solved in the latest commit - please pull and try again! If not, feel free to re-open this issue!

Cheers and so long
Lucas

PS: I saw that you edited your text quite a bit - and assume that you fixed all the problems that are now gone? In short:

• The error validating the config file is because newer versions of grenepipe tend to include more options, and I always make them required in the config file to make sure that users don't accidentally use outdated config files. That unfortunately means that the config file has to be fixed or re-done for every grenepipe version... but we are pre-1.0, so I feel this is a necessary evil...
• Input files with incompatible contigs: That seems to stem from changed reference files not fitting a particular run any more, or something. Usually, starting from scratch helps.

Let me know if there is anything else that does not work as it should ;-)

from grenepipe.

Hi Lucas yeah sorry about those edits, I ran into a couple problems that I was too quick to post about, exactly as you said one was about using the old config file and one was about not deleting all the output of a partially completed run. Thank you for the quick update, I am running now and have passed step 9 so I think it is solved.

from grenepipe.

Hey Ben,

no need to apologize, that is what the edit feature is for. I was probably just being overly thorough there ;-)

Glad to hear that it works now. NB: The "step number" is more or less meaningless though, as they can be reordered by snakemake, and differ very much depending on your config (i.e., which tools are used) and your data (both the number of samples and the number of reference sequences/contigs affect the total job count). So, a better way to check if a certain thing works now is to look for its rule name (and, if it only fails for certain data, for its input data or wildcards), to make sure that a step that failed earlier now works. Hope that makes sense.

So if there is still more trouble, let me know!
Lucas

from grenepipe.

Got it, it does. Well, the whole pipeline is working and producing usable output at the moment so I am happy ;)

from grenepipe.

Awesome! I feel that grenepipe is nearing a 1.0 release. It has been quite the struggle to fix all dependency issues for all users and clusters that it has been used on so far... One would think that the whole idea of conda is to fix those issues once and for all - as this issue (yet again) showcased, this is not true. So, thanks for being a patient beta-tester ;-)

from grenepipe.

No prob. I look forward to citing it knock on wood!

from grenepipe.