From be3d0574df8cf22be2b829b5c424d30548c05aa3 Mon Sep 17 00:00:00 2001 From: johnbamboobilly Date: Mon, 20 Aug 2018 20:15:29 -0700 Subject: [PATCH 1/4] Update CentOS setup guide --- sphinx_doc/setup_guide_centos.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/sphinx_doc/setup_guide_centos.rst b/sphinx_doc/setup_guide_centos.rst index defb97563..00da1ab37 100644 --- a/sphinx_doc/setup_guide_centos.rst +++ b/sphinx_doc/setup_guide_centos.rst @@ -151,6 +151,15 @@ Install PostgreSQL:: # restart : stop/start the database; used to read changes to core configuration files. # reload : reload pg_hba.conf file while keeping database running. + # login as superuser + su + + # Put the following code in the config file + vim /var/lib/pgsql/9.5/data/pg_hba.conf + local all all peer + host all all 127.0.0.1/32 ident + host all all ::1/128 md5 + # Start: sudo service postgresql-9.5 start @@ -166,6 +175,7 @@ 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 From 56f7d7493c5f4be1fb09998e2bae3e89abf5de08 Mon Sep 17 00:00:00 2001 From: Yi Hsiao Date: Fri, 31 Aug 2018 00:21:36 -0400 Subject: [PATCH 2/4] add troubleshooting document --- sphinx_doc/index.rst | 1 + sphinx_doc/setup_guide_centos.rst | 9 --------- sphinx_doc/troubleshooting.rst | 15 +++++++++++++++ 3 files changed, 16 insertions(+), 9 deletions(-) create mode 100644 sphinx_doc/troubleshooting.rst diff --git a/sphinx_doc/index.rst b/sphinx_doc/index.rst index 0cbecfd60..3b14a66de 100644 --- a/sphinx_doc/index.rst +++ b/sphinx_doc/index.rst @@ -33,6 +33,7 @@ Leveraging the `admin page of Django setup_guide user_guide deployment_guide + troubleshooting about Indices and tables diff --git a/sphinx_doc/setup_guide_centos.rst b/sphinx_doc/setup_guide_centos.rst index 00da1ab37..647c8b4d5 100644 --- a/sphinx_doc/setup_guide_centos.rst +++ b/sphinx_doc/setup_guide_centos.rst @@ -151,15 +151,6 @@ Install PostgreSQL:: # restart : stop/start the database; used to read changes to core configuration files. # reload : reload pg_hba.conf file while keeping database running. - # login as superuser - su - - # Put the following code in the config file - vim /var/lib/pgsql/9.5/data/pg_hba.conf - local all all peer - host all all 127.0.0.1/32 ident - host all all ::1/128 md5 - # Start: sudo service postgresql-9.5 start 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 From b7ce4b0577b235560dd506175dbdf13f3be9bd99 Mon Sep 17 00:00:00 2001 From: Yi Hsiao Date: Fri, 31 Aug 2018 00:40:30 -0400 Subject: [PATCH 3/4] add information about jbrowse integration --- i5k/settings.py | 3 ++- sphinx_doc/advanced_setup.rst | 13 +++++++++++++ sphinx_doc/setup_guide.rst | 1 + 3 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 sphinx_doc/advanced_setup.rst 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/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 From 56d40fba28f9abc27e8dbd4b2ff628bae4d4239d Mon Sep 17 00:00:00 2001 From: Yi Hsiao Date: Fri, 31 Aug 2018 00:50:02 -0400 Subject: [PATCH 4/4] add information of our github repos --- sphinx_doc/index.rst | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/sphinx_doc/index.rst b/sphinx_doc/index.rst index 3b14a66de..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