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luissian edited this page Oct 9, 2020 · 13 revisions

Create iSkyLIMS folder and modify permission settings

So far all the files and directories have been created with root.

To avoid permission issues when executing iSkyLIMS we need to change the owner of files to django user.

cd /srv
mkdir iSkyLIMS
chown django:bioinfo iSkyLIMS/
chmod 775 iSkyLIMS/
exit

NOTE: iSkyLIMS needs to execute schedule jobs using crontab.

For security reason, it is not recommended to use apache user to execute the schedule job. Instead, django user will be used to execute the user crontab.

The actions done on crontab requires to have a write access under the iSkyLIMs directory to save run files. For that reason iSyLIMS directory must have write granted for django user to save the necessary files.

Create the django project.

cd iSkyLIMS/
#clone the repository and init the submodules.
#clone repository
git clone https://github.com/BU-ISCIII/iSkyLIMS.git .
# Step inside your project: init and update submodules
git submodule init
git submodule update

NOTE: Make sure you have configured your public ssh key correctly in github settings, as submodules are updated using ssh connection instead of http. You can add it to your github account here.

As you can check on the /srv/iSkyLIMS directory, iSkyLIMS installation has the following modules:

  • iSkyLIMS_home
  • iSkyLIMS-drylab
  • iSkyLIMS-wetlab
  • django-utils

Static files

Each of the four modules has the set of required static files under /srv/iSkyLIMS//static. Some of them are common to all or some of the modules( stored under "iSkyLIMS_common_static"), while others related to a specific module. (are stored under /srv/iSkyLIMS/module/static/module/)

Important notes about the static files:

a) in the development phase: django development server ("runserver") fetch the static files in directories /srv/iSkyLIMS/module/static/module. Currently, and as a temporary solution we have stored the common files in the static directory of the four modules in order to let django reach them (so, yes, they are duplicated). Our intention is (logically) to have them in just one place, but until figuring out how to do it, a modification in one of the files should be replicated in the other copies of the same file. Sorry for the disturbance.

b) in the production phase: as you will see in the Apache section, django "collectstatus" fetches all of the modules static files and let them ready under /srv/iSkyLIMS/static. Just one instance of the common files is created (under (/srv/iSkyLIMS/static/iSkyLIMS_common_static))

Document Directory

Create the document folder to save all documents that needs to be handled by iSkyLIMS

mkdir -p /srv/iSkyLIMS/documents/wetlab/tmp
mkdir -p /srv/iSkyLIMS/documents/drylab
mkdir -p /srv/iSkyLIMS/logs
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