Comments (2)
Short answer, if you want to skip installation headaches and compilation time and are comfortable with Docker, use our Docker image. docker pull ctberthiaume/popcycle:4.17.0
. It's based on rocker/rstudio:4.2.1
. I usually run it with Rscript command-line scripts using a command similar to this:
docker run -it --rm -v $(pwd):/data ctberthiaume/popcycle:4.17.0 bash
And then cd to /data
where I have my scripts and data.
You could also use the Rstudio web IDE for R console/notebook access. See https://rocker-project.org/images/versioned/rstudio.html
If you want to make changes to the Docker image, for example by modifying popcycle or installing new dependencies, it's easy enough to make those changes and then docker commit
a new version of the image. The original image build process is captured here https://github.com/seaflow-uw/popcycle/blob/master/docker/Dockerfile
Otherwise, we have used devtools to install the pacakge, as you have also done. Unfortunately there are dependencies, I think related to flowcore, which significantly slow down the install process. Here's our script we use to do the install. https://github.com/seaflow-uw/popcycle/blob/master/setup.R. I believe it would be essentially equivalent to what you've done with some extra steps to make sure devtools and biocmanager are installed.
We've also started experimenting with using renv for dependency environment isolation and consistency. I would say that renv itself is still a work in progress and may not provide the most user-friendly experience. You can see the basic process for installing with renv in https://github.com/seaflow-uw/popcycle/blob/master/renv-first-install.R
renv is in fact what we use to build the Docker image.
from popcycle.
I'm satisfied with the installation instructions as of now.
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Related Issues (20)
- filter / gating parameters times are local HOT 1
- track all attempts to filter EVT files HOT 1
- warning message about "max(abs(i))" and "-Inf" when auto classifying HOT 1
- plot_map documentation
- zombie VCT results HOT 1
- Spurious errors when gating
- `get.opp.files` doesn't properly remove outliers HOT 2
- readSeaflow and get.opp.by.file have different signatures for similar tasks HOT 2
- readSeaflow doesn't check for too much data HOT 1
- Public interface exports too many functions
- Better build / install workflow for docs
- Better way to upgrade dependencies HOT 1
- Consider Apache Arrow to replace OPP when ready HOT 1
- Add tests for outlier filtering in get.* functions HOT 1
- Can't create OPP output directory when filtering HOT 1
- in `create_PSD`, add refractive indices for beads and unknow autmatically HOT 1
- Fix gating ID spacing in error message in `save_gating_plan`
- Make plan start_date more permissive
- `cmap_convert()` uses a deprecated `readr::write_csv` argument
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