Merge pull request #220 from NAL-i5K/third

Update document (CentOS setup and github repos information)
NAL-i5K · Sep 25, 2018 · 66f6f9e · 66f6f9e
2 parents 9dad733 + 56d40fb
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diff --git a/i5k/settings.py b/i5k/settings.py
@@ -183,9 +183,10 @@
     'large': {'verbose_name': 'Large (8 col)', 'width': 680, 'height': '', 'opts': ''},
 }
 
-# suit settings
+
 ENABLE_JBROWSE_INTEGRATION = False
 
+# customize some part of django-suit settings based on ENABLE_JBROWSE_INTEGRATION
 if ENABLE_JBROWSE_INTEGRATION:
     blast_models = (
             {'model': 'blastqueryrecord'},

diff --git a/sphinx_doc/advanced_setup.rst b/sphinx_doc/advanced_setup.rst
@@ -0,0 +1,13 @@
+Advanced Setup
+==============
+
+JBrowse/Apollo Linkout Integration
+----------------------------------
+
+In Genomics workspace, we have a linkout integration between BLAST and JBrowse/Apollo.
+You can directly go to corresponding sequence location through clicking entries in BLAST result table.
+To start using it, make change of :code:`ENABLE_JBROWSE_INTEGRATION` in :code:`i5k/settings.py`;
+
+.. code-block:: python
+
+   ENABLE_JBROWSE_INTEGRATION = True
diff --git a/sphinx_doc/index.rst b/sphinx_doc/index.rst
@@ -15,13 +15,20 @@ Leveraging the `admin page of Django
 <https://www.rabbitmq.com/>`_ and `Celery
 <http://www.celeryproject.org/>`_, it's much easier to manage the sequence databases and provide services to end-users.
 
+All source codes of genomics workspace are in `our github repo
+<https://github.com/NAL-i5K/genomics-workspace/>`_.
+
 .. note::
    You can try genomics workspace on our live services:
 
    * BLAST: https://i5k.nal.usda.gov/webapp/blast/
    * HMMER: https://i5k.nal.usda.gov/webapp/hmmer/
    * Clustal: https://i5k.nal.usda.gov/webapp/clustal/
 
+   In fact, the live services listed above are implemented by a customized version of genomics workspace.
+   You can check the source code of it in another github repo: `NAL-genomics-workspace
+   <https://github.com/NAL-i5K/NAL-genomics-workspace>`_.
+
 
 .. toctree::
    :maxdepth: 2
@@ -33,6 +40,7 @@ Leveraging the `admin page of Django
    setup_guide
    user_guide
    deployment_guide
+   troubleshooting
    about
 
 Indices and tables

diff --git a/sphinx_doc/setup_guide.rst b/sphinx_doc/setup_guide.rst
@@ -9,3 +9,4 @@ This is our introduction to this project.
 
    setup_guide_centos
    setup_guide_macos
+   advanced_setup
diff --git a/sphinx_doc/setup_guide_centos.rst b/sphinx_doc/setup_guide_centos.rst
@@ -166,6 +166,7 @@ Install PostgreSQL::
     create database django;
     create user django;
     grant all on database django to django;
+    ALTER USER django CREATEDB;
 
     # Connect to django database:
     \c django

diff --git a/sphinx_doc/troubleshooting.rst b/sphinx_doc/troubleshooting.rst
@@ -0,0 +1,15 @@
+Trouble Shooting
+================
+
+Q: I get an error message like: :code:`FATAL: Ident authentication failed`. How can I fix this ?
+
+A: It's because the setting of PostgreSQL database.
+Try to modify the config file :code:`pg_hba.conf`.
+For example, in PostgreSQL 9.5, the file is at :code:`/var/lib/pgsql/9.5/data/pg_hba.conf`.
+Make sure you change part of the content of it into something like:
+
+.. code-block:: none
+
+   local   all             all                               peer
+   host    all             all             127.0.0.1/32      ident
+   host    all             all             ::1/128           md5
Original file line number	Diff line number	Diff line change
Expand Up		@@ -9,3 +9,4 @@ This is our introduction to this project.

		setup_guide_centos
		setup_guide_macos
		advanced_setup