diff --git a/i5k/settings.py b/i5k/settings.py
index d935fdfb1..16b78437a 100755
--- 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
new file mode 100644
index 000000000..374fa2f3b
--- /dev/null
+++ 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
index 0cbecfd60..2e50eec79 100644
--- a/sphinx_doc/index.rst
+++ b/sphinx_doc/index.rst
@@ -15,6 +15,9 @@ Leveraging the `admin page of Django
`_ and `Celery
`_, 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
+`_.
+
.. note::
You can try genomics workspace on our live services:
@@ -22,6 +25,10 @@ Leveraging the `admin page of Django
* 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
+ `_.
+
.. 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
index 9101ba630..5409c22a3 100644
--- 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
index defb97563..647c8b4d5 100644
--- 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
new file mode 100644
index 000000000..ba67f65ac
--- /dev/null
+++ 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