scripts/README.md
In erictleung/dada2HPCPipe: DADA2 HPC Workflow Wrapper
SLURM Scripts
Overview
Here contains various SLURM scripts to run for each step of the pipeline.
Most of the scripts are preformatted and ready to go except the email
parameters to email you the results of the run.
To run most of the scripts, type in commands in this format:
sbatch test_pipeline.sh
Analysis Workflow
When running the scripts found in the test/ directory, it will generate a
particular directory structure to ease of looking at results and intermediate
steps.
The file structure should look similar to the following.
root/
|-- data/
|-- intermediate/
|-- metadata/
|-- README.md
|-- results/
|-- slurm_submit.sh
`-- src/
5 directories, 2 files
Transferring Results to Local
You can run the following command on your local terminal to get plots or other
data.
# Explanation:
# - scp - secure copy files
# - username@exahead.ohsu:~/plots/plot-1.png - modify path after `:` for
# files you want to transfer
# - where/you/want/file.png - this is the path on your local instance
scp username@exahead1.ohsu.edu:~/plots/plot-1.png where/you/want/file.png
erictleung/dada2HPCPipe documentation built on May 10, 2019, 1:19 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
SLURM Scripts
Overview
Here contains various SLURM scripts to run for each step of the pipeline.
Most of the scripts are preformatted and ready to go except the email parameters to email you the results of the run.
To run most of the scripts, type in commands in this format:
sbatch test_pipeline.sh
Analysis Workflow
When running the scripts found in the test/ directory, it will generate a
particular directory structure to ease of looking at results and intermediate
steps.
The file structure should look similar to the following.
root/
|-- data/
|-- intermediate/
|-- metadata/
|-- README.md
|-- results/
|-- slurm_submit.sh
`-- src/
5 directories, 2 files
Transferring Results to Local
You can run the following command on your local terminal to get plots or other data.
# Explanation:
# - scp - secure copy files
# - username@exahead.ohsu:~/plots/plot-1.png - modify path after `:` for
# files you want to transfer
# - where/you/want/file.png - this is the path on your local instance
scp username@exahead1.ohsu.edu:~/plots/plot-1.png where/you/want/file.png
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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