Step 1.1: Install dependencies
Dockerised setup
We are currently migrating to a Dockerised setup to further simplify setup and this documentation will be updated to reflect this approach soon.
Developed and tested on Ubuntu 14.04
easy import has been developed and tested on freshly installed Ubuntu 14.04. Most steps should run on alternate operating systems but
install-dependencies.sh
is OS/version specific.
- On a fresh install of Ubuntu 14.04 only the
git
package needs to be added manually:
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install git
- Then easy import can be
git clone
d into a local directory (namedei
in these instructions for brevity):
cd ~
git clone --recursive https://github.com/lepbase/easy-import ei
The --recursive
option to git clone
also clones the easy mirror and gff parser submodules into em
and gff
subdirectories, respectively. The gff parser is required during Stage 2 to handle the diversity of real-world .gff
files while easy mirror handles server/database/website setup and is the basis for all steps in Stages 1 and 4.
- Finally the easy mirror script
install-dependencies.sh
is used to fetch and install all dependencies.
Check configuration
before running any of these scripts, you should check the
Configuration options
and edit the relevant.ini
file to match your local setup.
cd ~/ei/em
sudo ./install-dependencies.sh ../conf/setup.ini
Configuration options
Only two stanzas of setup.ini
are used in Step 1.1:
[WEBSITE]
SERVER_ROOT = /ensembl
SERVER_ROOT
is the full path to the directory into which the Ensembl repositories will be cloned and from which an Ensembl instance will be hosted. The directory will be created if it does not already exist.
[ENSEMBL_USER]
WEB_USER_NAME = eguser
WEB_USER_PASS = password
If WEB_USER_NAME
is provided, a new user will be created with WEB_USER_PASS
, otherwise it defaults to the name of the user running the install-dependencies.sh
script. Ownership of the SERVER_ROOT
directory is transferred to WEB_USER_NAME
so if an alternate user is specified here, subsequent steps (none of which require root permissions) should be run as this alternate user.
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