Add new recipes

Update doc info
Ohter updates

Author: mikecormier

GGD-CLI.html

@@ -206,7 +206,7 @@ <h3 id="searchlabel">Quick search</h3>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="list-file.html">ggd get-files</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="list-file.html#using-ggd-list-files">Using ggd list-files</a></li>
+<li class="toctree-l2"><a class="reference internal" href="list-file.html#using-ggd-get-files">Using ggd get-files</a></li>
 <li class="toctree-l2"><a class="reference internal" href="list-file.html#examples">Examples</a></li>
 </ul>
 </li>

_sources/check-recipe.rst.txt

@@ -27,17 +27,17 @@ check-recipe arguments:
 | ggd check-recipe      | Convert a ggd recipe created from `ggd make-recipe` into a data package. Test    |
 |                       | both ggd data recipe and data package                                            |
 +=======================+==================================================================================+
-| -h, --help            |   show this help message and exit                                                |
+| ``-h``, ``--help``    |   show this help message and exit                                                |
 +-----------------------+----------------------------------------------------------------------------------+
-| -d, --debug           |  (Optional) Set the stdout log level to debug                                    | 
+| ``-d``, ``--debug``   |  (Optional) Set the stdout log level to debug                                    | 
 +-----------------------+----------------------------------------------------------------------------------+
-| -du, --dont_uninstall |   (Optional) By default the newly installed local ggd                            |
-|                       |   data package is uninstalled after the check has                                |
-|                       |   finished. To bypass this uninstall step (to keep the                           | 
-|                       |   local package installed) set this flag "--                                     |
-|                       |   dont_uninstall"                                                                |
+| ``-du``,              | (Optional) By default the newly installed local ggd                              |
+| ``--dont_uninstall``  | data package is uninstalled after the check has                                  |
+|                       | finished. To bypass this uninstall step (to keep the                             | 
+|                       | local package installed) set this flag "--                                       |
+|                       | dont_uninstall"                                                                  |
 +-----------------------+----------------------------------------------------------------------------------+
-| recipe_path           |   **Required** Path to recipe directory (can also be path to the .bz2)           |
+| ``recipe_path``       |   **Required** Path to recipe directory (can also be path to the .bz2)           |
 +-----------------------+----------------------------------------------------------------------------------+
 
 

_sources/contribute-recipe.rst.txt

@@ -75,7 +75,7 @@ The following will outline steps used to create the hg19-gaps ggd data recipe:
         tabix hg19-gaps-ucsc-v1.bed.gz
 
 * In this data processing script please change the resulting data file names to be short and include all necessary
-  genomic file extentions. (See the NOTE bellow) 
+  genomic file extensions. (See the NOTE bellow) 
 
 You should run the script to make sure it works and that the processed files are what you expect them to be.
 
@@ -84,17 +84,17 @@ You should run the script to make sure it works and that the processed files are
 
        The final data file names will be changed to reflect the new ggd recipe name. To keep the data file name as 
        short as possible please rename data files to include only a short name and the genomic file extensions. The name
-       will be replaced with the ggd recipe name, and the genomic file extention will be kept. For example, in the 
-       hg19-gaps example above *gaps.bed.gz* and the tabix companion *gaps.bed.gz.tbi* will be renmaed to *hg19-gaps.bed.gz*
-       and *hg19-gaps.bed.gz.tbi*. Because of the complexities with genomic file extentions all extentions will be retained
+       will be replaced with the ggd recipe name, and the genomic file extension will be kept. For example, in the 
+       hg19-gaps example above *gaps.bed.gz* and the tabix companion *gaps.bed.gz.tbi* will be renamed to *hg19-gaps.bed.gz*
+       and *hg19-gaps.bed.gz.tbi*. Because of the complexities with genomic file extensions all extensions will be retained
        and only the beginning name before the first '.' will be replaced with the recipe name. 
 
 
     .. note:: 
 
         Make sure that any intermediate files or other files used for data processing are removed after processing. Only the 
         final processed data files should remain once the script has finished. If extra files are not removed they will be
-        added as members of the data recipe, which is most likley un-wanted and un-needed. 
+        added as members of the data recipe, which is most likely un-wanted and un-needed. 
 
 
 3. Create a ggd recipe using the ggd cli