update docs

pepkit · Feb 28, 2019 · 33810dd · 33810dd
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diff --git a/docs/README.md b/docs/README.md
@@ -1,6 +1,6 @@
-[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
+# <img src="img/geofetch_logo.svg" class="img-header">
 
-# <img src="img/geofetch_logo.svg" class="img-fluid" style="max-height:45px; margin-top:-15px; margin-bottom:-10px">  geofetch
+[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
 `geofetch` is a command-line tool that does two things when given one or more GEO/SRA accessions:
 

diff --git a/docs/faq.md b/docs/faq.md
@@ -0,0 +1,13 @@
+# FAQ
+
+
+## I get an error: `geofetch: command not found` after installing. Why isn't the `geofetch` executable in my path?
+
+
+By default, Python packages are installed to `~/.local/bin`. You can add this location to your path by appending it:
+
+```
+export PATH=$PATH:~/.local/bin
+```
+
+Add this line to your `.bashrc` or `.profile` to make it permanent.
diff --git a/docs/img/geofetch_logo_dark.svg b/docs/img/geofetch_logo_dark.svg
diff --git a/docs/tutorial.md b/docs/tutorial.md
@@ -1,4 +1,4 @@
-# geofetch tutorial
+# <img src="../img/geofetch_logo.svg" class="img-header">  tutorial
 
 ## Prerequisites
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -1,4 +1,4 @@
-# <img src="../img/geofetch_logo.svg" class="img-fluid" style="max-height:35px; margin-top:-15px; margin-bottom:-10px">  usage reference
+# <img src="../img/geofetch_logo.svg" class="img-header">  usage reference
 
 `geofetch` command-line usage instructions:
 
@@ -9,7 +9,7 @@
 usage: geofetch [-h] -i INPUT [-n NAME] [-m METADATA_FOLDER] [-f]
                 [--just-metadata] [-r] [--acc-anno] [--use-key-subset] [-x]
                 [--config-template CONFIG_TEMPLATE] [-p] [-g GEO_FOLDER]
-                [-b BAM_FOLDER]
+                [-b BAM_FOLDER] [-P PIPELINE_INTERFACES]
 
 Automatic GEO SRA data downloader
 
@@ -40,12 +40,15 @@ optional arguments:
                         setting instead treats each run as a separate sample
   --config-template CONFIG_TEMPLATE
                         Project config yaml file template.
-  -p, --processed       Download processed data (Default: download raw data).
+  -p, --processed       Download processed data [Default: download raw data].
   -g GEO_FOLDER, --geo-folder GEO_FOLDER
                         Optional: Specify a location to store processed GEO
                         files [Default: $GEODATA:]
   -b BAM_FOLDER, --bam-folder BAM_FOLDER
                         Optional: Specify folder of bam files. Geofetch will
                         not download sra files when corresponding bam files
                         already exist. [Default: $SRABAM:]
+  -P PIPELINE_INTERFACES, --pipeline_interfaces PIPELINE_INTERFACES
+                        Optional: Specify the filepath of a pipeline interface
+                        yaml file. [Default: null]
 ```
diff --git a/docs/usage_template.md b/docs/usage_template.md
@@ -1,4 +1,4 @@
-# <img src="../img/geofetch_logo.svg" class="img-fluid" style="max-height:45px; margin-top:-15px; margin-bottom:-10px">  usage reference
+# <img src="../img/geofetch_logo.svg" class="img-header">  usage reference
 
 `geofetch` command-line usage instructions:
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -13,6 +13,7 @@ nav:
     - How to control data location: howto-location.md
   - Reference:
     - Usage: usage.md
+    - FAQ: faq.md
     - Support: support.md
     - Contributing: contributing.md
   - Changelog: changelog.md

diff --git a/setup.py b/setup.py
@@ -56,7 +56,7 @@ def get_static(name, condition=None):
     name=PACKAGE,
     packages=[PACKAGE],
     version=version,
-    description="A ",
+    description="Downloads data and metadata from GEO and SRA and creates standard PEPs.",
     long_description=long_description,
     classifiers=[
         "Development Status :: 4 - Beta",