ex-294 (cgates): update rtd theme; removed obsolete files

umich-brcf-bioinf · Sep 22, 2015 · c4e9005 · c4e9005
1 parent 8ee0af9
commit c4e9005
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diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs
@@ -1,5 +1,2 @@
 eclipse.preferences.version=1
 encoding//doc/conf.py=utf-8
-encoding//doc/css/jacquard_theme.css=UTF-8
-encoding//doc/jacquard_unminified=UTF-8
-encoding//doc/theme_unminified=UTF-8
diff --git a/doc/command_details.rst b/doc/command_details.rst
@@ -18,15 +18,15 @@ work for any VCFs. Each of these commands is described in detail in the
 following pages.
 
 
-General usage
-^^^^^^^^^^^^^
-``usage: jacquard <SUBCOMMAND> [ARGUMENTS] [OPTIONS]``
+**General usage**
+::
 
+   jacquard <SUBCOMMAND> [ARGUMENTS] [OPTIONS]
 
 For help on a specific command:
+::
 
-
-``jacquard <SUBCOMMAND> --help``
+   jacquard <SUBCOMMAND> --help
 
 
 * Jacquard first writes output files to a temporary directory and only copies
@@ -35,8 +35,8 @@ For help on a specific command:
   messages are only written to the log file (unless --verbose specified).
 
 
-Input File Conventions
-^^^^^^^^^^^^^^^^^^^^^^
+**Input File Conventions**
+
 * Jacquard assumes that the first element of the filename (up to the first dot)
   is a patient identifier. For example:
 

diff --git a/doc/css/jacquard.css b/doc/css/jacquard.css
diff --git a/doc/css/jacquard_theme.css b/doc/css/jacquard_theme.css