README

Requirements

Environment

Expvip runs on Unix-Like environments (Linux distribution or mac).
The project doesn’t run on Windows OS

Programs

The following must be installed on your environment (minimum requirements):

Git
Ruby 2.7
Rails 6.0
Nodejs v14
yarn 1.22
MySQL 8.0 (along with its development files - libmysqlclient-dev)
Kallisto 0.44.0 (optional)

Get Kallisto from here

Data

Data required for setting up expvip can be downloaded form here

Setting up expVIP

Follow these steps:

Software code

1. Clone the project using Git to the default repository. git clone {SSH/URL}
2. Run npm/yarn install using the terminal to install the JavaScript dependencies and then run npm/yarn bundle.
3. Run bundle install using the terminal to install the gem dependencies.

Database set up

1. Mysql Database: Set your mysql database with user and password according to your Config/Database.yml file

database: expvip
username: expvipUSR
password: expvipPWD

2. Run the following rake tasks to create the database and tables.

rake db:setup
rake db:migrate

3. Run sequenceserver to install NCBI Blast+ binaries if not installed and to create the database.
   Give the path to the .fasta file (e.g. Triticum_aestivum.IWGSC2.26.cdna.all.fa or IWGSC_v1.1_ALL_20170706_transcripts.fasta) where you have downloaded it to your machine for creating the database.
4. Run the following rake task to load the factors from the file FactorOrder.tsv using rake load_data:factor[{path-to-FactorOrder.tsv}]
5. Run the following rake task to load the metadata from the file default_metadata.txt using rake load_data:metadata[{path-to-default_metadata.txt}]
6. Run the following rake task to load the gene set from the file (e.g. Triticum_aestivum.IWGSC2.26.cdna.all.fa) using rake load_data:ensembl_genes[{gene-set-name},{path-to-The-file-containing-gene-set-data}]
7. Run the following rake task to load the homology data from the file (compara_homolgy.txt) using rake load_data:homology_pairs[{gene-set-name},{path-to-the-file-containing-homology-data}]. Note that the gene names are not the same as the transcript names, they correspond to the gene name. The file can be genrated with ensembl compara, using the following query:

   SELECT 
   	homology_member.homology_id, cigar_line, perc_cov, perc_id, perc_pos, 
   	gene_member.stable_id as genes, 
   	gene_member.genome_db_id
   
   FROM 
       homology_member 
   INNER JOIN homology USING (homology_id) 
   INNER JOIN method_link_species_set USING (method_link_species_set_id) 
   INNER JOIN gene_member USING (gene_member_id)
   WHERE method_link_species_set.name="T.aes homoeologues";

8. Start MongoDB service in order to populate the table with data. sudo service mongod start
9. Run the following rake task to load the value data into MongoDB from the file containing the value data (final_output_tmp.txt)
   using rake load_data:values_mongo[First Run,{gene-set-name},{tmp/counts},}{path-to-the-file-containing-tmp-or-counts-value-data}].

Run expVIP

After you have followed all the mentioned steps. Run the following command npm/yarn start and navigate to localhost:3000 in your browser.

Important Note

If any step was wrong or missed or needed to be modified please create an issue on expvip repository on GitHub and explain your proposed changes to the documentation.

Contributing

Please submit all issues and pull requests to the homonecloco/expvip-web repository!

Support

If you have any problem or suggestion please open an issue here.

License

The MIT License

Copyright (c) 2015, Ricardo H. Ramirez-Gonzalez

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.