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Delete or move to IFTPipeline readme #359

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cpaniaguam opened this issue Nov 30, 2023 · 1 comment
Closed

Delete or move to IFTPipeline readme #359

cpaniaguam opened this issue Nov 30, 2023 · 1 comment
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🧹 clean up code clean ups and other quick fixes

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@cpaniaguam
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There are sections discussing fetchdata, the cli, and some old stuff about snakemake in the readme. I think parts of this could be moved to the IFTPipeline repo and the remaining deleted altogether.

## Fetch Data
The [`fetchdata.sh`](/scripts/fetchdata.sh) script requires the utilities [`gdal`](https://gdal.org/) and [`proj`](https://proj.org/). This repository includes a brewfile for ease of installation on MacOS. To install `gdal` and `proj` via homebrew, first [install homebrew](https://brew.sh/), then run `brew bundle install`
### Example
```
$ ./scripts/fetchdata.sh -o data -s 2022-05-01 81 -22 79 -12
```
## Commandline
To call each step of Ice Floe Tracker pipeline from the command line you can run:
```
./scripts/ice-floe-tracker.jl
```
Each step of the pipeline is implemented as a command to the script. Most commands take a metadata file, input directory, and output directory.
For example:
```
./scripts/ice-floe-tracker.jl landmask <METADATA FILE> <INPUT DIR> <OUTPUT DIR>
```
## Snakemake
Snakemake is used to encode the entire pipeline from start to finish. Snakemake relies on the command line scripts to automate the pipeline. The snakemake file should be suitable for runs on HPC systems. To run snakemake locally, run the following from a terminal in the root of this project:
```
snakemake -c<NUM CORES>
```

@cpaniaguam cpaniaguam added the 🧹 clean up code clean ups and other quick fixes label Nov 30, 2023
@tdivoll
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tdivoll commented Jan 18, 2024

Closed by #360

@tdivoll tdivoll closed this as completed Jan 18, 2024
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