QUICKSTART.rst: update section Automating downloading and updating the network.

2 files changed, 12 insertions, 13 deletions

diff --git a/brain.documentation/QUICKSTART.rst b/brain.documentation/QUICKSTART.rst
index c177377..4a5d95f 100644
--- a/brain.documentation/QUICKSTART.rst
+++ b/brain.documentation/QUICKSTART.rst
@@ -7,7 +7,7 @@ B R A I N
 :Version: 0.1.6 of 2022-10-09

 	  

 

-*Revision history: 9 June 2017, 22 June 2017, 4 July 2017, 11 July 2017 (created Section Drawing sub-networks), 18 July 2017 (created Section Uploading peak files), 10 October 2017 ('Enter a set of genes' under Section Exploring the network; created Section uRNA), 24 Jan 2018 (Enter 'AT1G24260 AGL9;SEP3 tissue specific tau 1.9' under Section Exploring the network), 3 August 2019 (design considerations), 5 August 2019 (updated create_edges0.py, added a section FAQs), 7 August 2019 (files needed for drawing a scatterplot online), 11 August 2019 (added information for correlation_per_group_fixed_number.R), 22 November 2019 (review and revise the entire content of this documentation), 4 April 2020 (use html_network.py to generate static html pages that contain a gene's regulators and regulatees; use cron job to copy these files to the web application), 6 February 2021 (write a section describing the running environment for brain), 9 October 2022 (remove PARAMETER_FOR from PARAMETER_FOR_BUILDRMATRIX_RENEW_INTERVAL)*

+*Revision history: 9 June 2017, 22 June 2017, 4 July 2017, 11 July 2017 (created Section Drawing sub-networks), 18 July 2017 (created Section Uploading peak files), 10 October 2017 ('Enter a set of genes' under Section Exploring the network; created Section uRNA), 24 Jan 2018 (Enter 'AT1G24260 AGL9;SEP3 tissue specific tau 1.9' under Section Exploring the network), 3 August 2019 (design considerations), 5 August 2019 (updated create_edges0.py, added a section FAQs), 7 August 2019 (files needed for drawing a scatterplot online), 11 August 2019 (added information for correlation_per_group_fixed_number.R), 22 November 2019 (review and revise the entire content of this documentation), 4 April 2020 (use html_network.py to generate static html pages that contain a gene's regulators and regulatees; use cron job to copy these files to the web application), 6 February 2021 (write a section describing the running environment for brain), 9 October 2022 (remove PARAMETER_FOR from PARAMETER_FOR_BUILDRMATRIX_RENEW_INTERVAL, update section Automating downloading and updating the network)*

 

 

 .. contents::

@@ -130,34 +130,33 @@ In the above three parameter files, the user needs to specify paths to certain f
 Automating downloading and updating the network

 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

-Instead of manually execute python update_network.py from time to time, we can make a *cron job* for it.  To do so,

+Instead of manually execute python update_network.py from time to time, we can schedule a *cron job* for it.  To do so,

 

 - In the terminal, type::

 

      	 crontab -e

 

 

-- Append the following line::

+- Append the following lines::

 

-    59 23 * * * cd /home/lanhui/brain/Code &&  'ps -eF | grep python3 | grep update_network' || python3 update_network.py

-    1 6 * * *  cd /home/lanhui/brain/Code && python3 download_and_map.py

+    5 23 * * * cd /home/lanhui/brain/Code && flock -n /tmp/brain.lockfile ./update_network.py

+    5 1 * * * cd /home/lanhui/brain/Code && python3 update_network_by_force.py

+    1 6 * * * cd /home/lanhui/brain/Code && python3 download_and_map.py

 

+update_network.py will run every day at 23:05 pm (if it is not already running).

 

+update_network_by_force.py will run every day at 1:05 am.  update_network_by_force.py does not actually compute edges.  It just collects newly generated edges by update_network.py, so it will take much shorter time to finish.

 

-This makes update_network.py run every day at 23:59pm, and makes download_and_map.py run every day at 6:01am.

+download_and_map.py will run every day at 6:01 am.

 

-Don't forget to change '/home/lanhui/brain' to the path to your working directory.

-

-The first line in the crontab is too long.  The purpose is to run update_network.py only if it is not already running.  There is a better method (being used now)::

-  

-    59 23 * * * cd /home/lanhui/brain/Code &&  flock /tmp/brain.lockfile ./update_network.py  

+*Don't forget to change '/home/lanhui/brain' to the path to your working directory.*

 

 We should change update_network.py to be executable (chmod u+x update_network.py).  Also add a shebang line (#! /usr/bin/python3) on the top of update_network.py.

 

-update_network.py could take a few days to finish, if there are lots of (e.g. millions) binding evidences to check.  In order to harvest updated edges each day, use update_network_by_force.py, which will be only interested in incorporating newly computed edges without actually computing them (computing them is the job of update_network.py).

+update_network.py could take a few days (even weeks) to finish, if there are lots of (e.g. millions) binding evidences to check.  In order to harvest updated edges each day, use update_network_by_force.py, which will be only interested in incorporating newly computed edges without actually computing them (computing them is the job of update_network.py).

 

 

-The files generated above (i.e., edges.txt, edges.sqlite, and GeneID.html) must be copied to the web application folder for it to work properly::

+The files generated above (i.e., edges.txt, edges.sqlite, and GeneID.html) must be copied to the Web Application folder (/var/www/brain) for it to work properly.  Edit the crontab file using the root's account, as follows::

 

   

   15 9,17 * * * sudo lsof /home/lanhui/brain/Data/temp/edges.txt || sudo cp /home/lanhui/brain/Data/temp/edges.txt /var/www/brain/brain/static/edges/edges.txt

diff --git a/index.html b/index.html
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/index.html