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Container & documentation #3
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Do the recent updates answer your question? I believe the small example dataset is present in tests and can be run along these lines:
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Currently doing other things. Will revisit this at a later point. Thank you for replying though! |
On a similar note, adding the R package dependencies to the FAQ would be helpful. I was moving fast so didn't realize it also needed For what it's worth, I didn't do a full container but used conda-forge to install the dependencies for only this project, and it was nice. You could even set up a maegatk conda(-forge) package and it would take care of installing all the binary dependencies for future users |
added some notes on the R package install-- thanks for that note @JZL I don't have any direct experience making a conda package but would welcome a pull request from anyone for this! |
Hi, These are just some scattered thoughts getting it to run. I can make a more formal PR with these changes in the future To get this running for future people. You also need to install Additionally:
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I am having a similar issue when trying to run this small test dataset as described. Is there a specific snakemake version that maegatk has been tested with? Trying to isolate what is going wrong for me. The pipeline seems to run fine for the 'splitting' part, but then fails to submit the snakemake job and perform the remaining analyses:
where the above is the end of the log message. If I look in "final/" this is all I see:
My environment for running maegatk looks like this and is based on your description in the readme.
Thanks! |
@alecpnkw do you have any log files in logs/? My snakemake version is 7.18.2, but I don't think maegatk was ever tested with a particular version of it. If nothing informative comes from logs/, try modifying
If that won't work either, try this:
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Thanks, knowing that a later snakemake versions runs in helpful. I'd like to try to keep the source the same as v0.2.0 for deployment reasons but happy to test if I can't get anything else to work. Based on the issues you linked I tweaked my environment to change the ruamel.yaml version to 0.17 and now am getting better results (!). It looks like the final output is there (
Still, I am not getting any logs inside |
It seems your test job has finished successfully. |
Awesome, thanks. Is there someplace I can access a test |
Hi there @noranekonobokkusu. I came across similar problems using the test data as you did in issue #5 . First I uninstalled ruamel.yaml (current version 0.18.6) and then installed ruamel.yaml==0.17 and still get the same issues, so back to 0.18.6. I've tried snakemake 6.6.1 and 7.18.2. I tried specifying snakemake path in the updated cli.py file, and the modification to the oneSample_maegatk.py as suggested. Still I get the same error output: Error in checkGrep(grep(".A.txt", files)) : base.maegatk.log does not show errors, however I do not see the .rds file in /final. but in maegatk.snakemake_gather.log I get an error about "Error in rule make_final_sparse_matrices"and in maegatk.snakemake_scatter.log some Java and samtools error. base.maegatk.log What would your recommendation be to get this to run? I'd really like to use this tool! |
Hi @Spirometra sorry for the late reply. |
Hi,
would it be possible that you provide a container with a full environment to get the pipeline running, please? A small example dataset would also help a lot.
Moreover, the pipeline parameters and flags etc are not document yet.
Thank you very much!
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