the work flow

ex novo

pre-requisites (see https://intermine.readthedocs.io/en/latest/system-requirements/software/)

Software	>=	Purpose
Git	        1.7	check out and update source code
Java SDK	8	build and use InterMine
Tomcat	        8.5.x	website
PostgreSQL	9.3.x	database
Perl	        5.8.8	run build scripts
Maven	        3.0.5	manage local dependencies
SOLR	        7.2.1	search engine

We also require an already created postgres user for the various databases.

Alternatively sudo powers to create the user as postgres

1) choose a name

e.g. Iris

2) create a github repo with you mine name

use script make_mine in repository intermine-scripts e.g.

./intermine-scripts/make_mine IrisMine 

3) create a mine properties file

to store database connection info, plus tomcat manager u/p and initial userprofile adm TODO

4) create needed databases

TODO e.g. createdb -h localhost -U modmine ithrivemine createdb -h localhost -U modmine items-ithrivemine createdb -h localhost -U modmine userprofile-ithrivemine buildDB buildUserdb

5) update project.xml (with your sources)

6) if you need additional sources

not available in the core intermine, see https://github.com/intermine/intermine/tree/dev/bio/sources: a) create a new repository e.g.

irismine-sources

b) for each new source you need to load:

• create a skeleton for the loader of the source use the script ./intermine-scripts/make_source $SOURCE_NAME $SOURCE_TYPE

where SOURCE_TYPE can be:

db	To load data directly from another database
gff	for GFF files
fasta	for FASTA files
obo	for Ontology files
custom-file	If you have a data file and want to parse using Java
intermine-items-xml-file	If you have a data file and want to parse using a language other than Java
intermine-items-large-xml-file	Same as above but the file is very very large

7) decide if you want to run any post-process

see https://intermine.readthedocs.io/en/latest/database/database-building/post-processing/

8) Set up the solr search index

see https://intermine.readthedocs.io/en/latest/system-requirements/software/solr/

9) build your mine

use project_build

10) deploy your webapp

• tomcat is running
• from your irismine directory run ./gradlew cargoDeployRemote (the first time) or ./gradlew cargoRedeployRemote after that