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laurenkleine / taxonomy-nf

The Stenglein Lab Standard Taxonomic Assessment Pipeline taxonomically assigns reads in a NGS dataset that remain after filtering host sequences.
https://laurenkleine.github.io/shpinx-nf-doc-taxonomy/
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Files created by docker are owned by root, causing problems when nextflow run w/ docker and w/out sudo #8

Open stenglein-lab opened 6 years ago

stenglein-lab commented 6 years ago

Most of the time, users won't have sudo access, so won't be able to run the nextflow pipeline via sudo. When I ran the nextflow pipeline as mdstengl w/out sudo, I got "WARN: Failed to publish file:" warnings from the FASTQC process (see below for output).

This seems to be because files created via docker are owned by root: mdstengl@stengleinlab101:~/analyses/taxonomy-nf$ ll /home/mdstengl/analyses/taxonomy-nf/work/1b/ad637e4191e2edd6dad17ccb748cb0/Croc7776_subset_R1_fastqc.html -rw-r--r-- 1 root root 341K Apr 17 17:04 /home/mdstengl/analyses/taxonomy-nf/work/1b/ad637e4191e2edd6dad17ccb748cb0/Croc7776_subset_R1_fastqc.html

When I googled about this, it appears that there are some workarounds, but I'm not entirely sure what the best approach is. See, e.g.:

https://www.google.com/search?safe=off&q=docker+creates+files+as+root

Ultimately, it will be necessary that the pipeline be runnable by users without sudo access.

mdstengl@stengleinlab101:~/analyses/taxonomy-nf$ nextflow run main_practice_docker.nf -profile docker -resume -with-report -with-trace N E X T F L O W ~ version 0.27.4 Launching main_practice_docker.nf [chaotic_mcnulty] - revision: 9533e07c3d [warm up] executor > local [01/dbd2f7] Cached process > RunCutAdapt (Croc7776_subset) [1b/ad637e] Cached process > RunPreFastQC (Croc7776_subset) WARN: Failed to publish file: /home/mdstengl/analyses/taxonomy-nf/work/1b/ad637e4191e2edd6dad17ccb748cb0/Croc7776_subset_R1_fastqc.html; to: /home/mdstengl/analyses/taxonomy-nf/results/FastQCResults/Pre/Croc7776_subset_R1_fastqc.html [link] -- See log file for details WARN: Failed to publish file: /home/mdstengl/analyses/taxonomy-nf/work/01/dbd2f72079c533437102fa89462a1a/Croc7776_subset.R1.fastq; to: /home/mdstengl/analyses/taxonomy-nf/results/CutAdaptResults/Croc7776_subset.R1.fastq [link] -- See log file for details WARN: Failed to publish file: /home/mdstengl/analyses/taxonomy-nf/work/1b/ad637e4191e2edd6dad17ccb748cb0/Croc7776_subset_R1_fastqc.zip; to: /home/mdstengl/analyses/taxonomy-nf/results/FastQCResults/Pre/Croc7776_subset_R1_fastqc.zip [link] -- See log file for details WARN: Failed to publish file: /home/mdstengl/analyses/taxonomy-nf/work/01/dbd2f72079c533437102fa89462a1a/Croc7776_subset.R2.fastq; to: /home/mdstengl/analyses/taxonomy-nf/results/CutAdaptResults/Croc7776_subset.R2.fastq [link] -- See log file for details WARN: Failed to publish file: /home/mdstengl/analyses/taxonomy-nf/work/1b/ad637e4191e2edd6dad17ccb748cb0/Croc7776_subset_R2_fastqc.html; to: /home/mdstengl/analyses/taxonomy-nf/results/FastQCResults/Pre/Croc7776_subset_R2_fastqc.html [link] -- See log file for details WARN: Failed to publish file: /home/mdstengl/analyses/taxonomy-nf/work/1b/ad637e4191e2edd6dad17ccb748cb0/Croc7776_subset_R2_fastqc.zip; to: /home/mdstengl/analyses/taxonomy-nf/results/FastQCResults/Pre/Croc7776_subset_R2_fastqc.zip [link] -- See log file for details

laurenkleine commented 6 years ago

I changed the processes that have "link" to "copy" and I stopped getting the error message on my end. Is that the case on your end? (I've updated main_practice_docker.nf on the repository with this edit)

Do you still get the same permissions error, or a different one, or one at all?