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Update container version #158

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lekoenig opened this issue Sep 8, 2022 · 3 comments
Open
1 of 2 tasks

Update container version #158

lekoenig opened this issue Sep 8, 2022 · 3 comments
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pipeline targets and/or snakemake pipeline and managing environments

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@lekoenig
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lekoenig commented Sep 8, 2022

There are currently two versions of the container on caldera: do-ml_v0.2.sif and do-ml_v0.3.sif. Perhaps if we're going to update the version to v0.4 we should go ahead and update the container to add a few additional libraries that are used for visualization purposes, including {USAboundaries}, {ggspatial}, {cowplot}, {patchwork}, and {yaml}.

  • update container to add new libraries in v0.5 (Jeff)
  • use singularity pull docker:://jsadler2/do-ml:v0.x to update the version on caldera (Lauren)
@lekoenig lekoenig added the pipeline targets and/or snakemake pipeline and managing environments label Sep 8, 2022
@lekoenig
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lekoenig commented Nov 3, 2022

{yaml} seems to be installed on tallgrass, but the package version isn't recent enough to include some formatting options that I was expecting. I suggest we install this version if not the latest release:

> packageVersion("yaml")
[1] ‘2.3.5

@jsadler2
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I've updated the docker image with those additional packages: jsadler2/do-ml:v0.5. So you should be able to now do singularity pull docker://jsadler2/do-ml:v0.5 to get the latest.

@lekoenig
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Thanks, Jeff! I pulled down the updated image and updated launch-rstudio-container.slurm to use the do-ml_v0.5.sif file. Is there a way to confirm that the new image is being used?

I tried to run tar_make(p3_site_map_png) but am still getting an error about the missing USAboundaries library.

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