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Tom Roche committed f65feba

update README after successful uber_driver from repo

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 To run this code,
 
-1. `git clone` this repo.
+1. `git clone` this repo. (See commandlines on the project homepage, where you probably are now.)
 1. `cd` to its working directory (where you cloned it to).
-1. Open the [bash utilities][bash_utilities.sh] in an editor! You will probably need to edit the functions `setup_paths` and `setup_apps` to make it work on your platform. Notably you will probably want to point it to your PDF viewer and NCL and R executables.
+1. Setup your applications and paths.
+    1. Download a copy of [these bash utilities][bash_utilities.sh] to the working directory.
+    1. Open the file in in an editor! You will probably need to edit its functions `setup_paths` and `setup_apps` to make it work on your platform. Notably you will want to point it to your PDF viewer and NCL and R executables.
     1. You may also want to open the [driver (bash) script][GEIA_driver.sh] in an editor and take a look. It should run Out Of The Box, but you might need to tweak something there. In the worst case, you could hardcode your paths and apps in the driver.
     1. Once you've got it working, you may want to fork it. If so, you can automate running your changes with [uber_driver.sh][] (changing that as needed, too).
 1. Run the driver:
-    `$ ./GEIA_driver.sh`
-1. This will download input, then run
+        `$ ./GEIA_driver.sh`
+    This will download input (and possibly `git clone` the `[regrid_utils][regrid_utils repository]`), then run
     * an [R script][reformat_GEIA_to_netCDF.r] to convert the input to a [netCDF][] file, and plot it. The driver should display [a PDF][reformatting plot] if properly configured.
     * another [R script][regrid_global_to_AQMEII.r] to regrid the netCDF, and plot the output. The driver should display [a PDF][regridding plot] if properly configured. This PDF currently has 2 pages (p1 using `raster::plot` and p2 using `fields::image.plot`).
     * an [NCL script][retemp_reunit.ncl] to [convert regridded concentrations][GEIA input processing @ project wiki] to units appropriate for [CMAQ][CMAQ @ CMAS].
                    global        NAs  AQMEII-NA        NAs     out/in
                  3.60e+06      28657   1.06e+06      90768   2.96e-01
 
-[bash_utilities.sh]: https://bitbucket.org/tlroche/geia_regrid/src/750cf565f859a51e72c616dfbc4d8bf841ff7f06/bash_utilities.sh?at=master
+[bash_utilities.sh]: https://bitbucket.org/tlroche/regrid_utils/src/8e8da93bc64962c8ca8abe1a445d261434ac831f/bash_utilities.sh?at=master
 [GEIA_driver.sh]: https://bitbucket.org/tlroche/geia_regrid/src/750cf565f859a51e72c616dfbc4d8bf841ff7f06/GEIA_driver.sh?at=master
 [uber_driver.sh]: https://bitbucket.org/tlroche/geia_regrid/src/750cf565f859a51e72c616dfbc4d8bf841ff7f06/uber_driver.sh?at=master
+[regrid_utils repository]: https://bitbucket.org/tlroche/regrid_utils
 [reformatting plot]: https://bitbucket.org/tlroche/geia_regrid/downloads/GEIA_N2O_oceanic.pdf
 [regridding plot]: https://bitbucket.org/tlroche/geia_regrid/downloads/GEIA_N2O_oceanic_regrid.pdf
 [GEIA input processing @ project wiki]: https://github.com/TomRoche/cornbeltN2O/wiki/Simulation-of-N2O-Production-and-Transport-in-the-US-Cornbelt-Compared-to-Tower-Measurements#wiki-input-processing-GEIA