title	header-includes	output
HIHISIV - The database of gene expression in HIV and SIV host immune response	\usepackage{titling} \pretitle{\begin{center} \includegraphics[width=2in,height=2in]{../hihisiv_other_parts/e_figures/logoDB.png}\LARGE\\} \posttitle{\end{center}} \usepackage{pdflscape} \newcommand{\blandscape}{\begin{landscape}} \newcommand{\elandscape}{\end{landscape}}	html_document pdf_document toc toc_depth true 4 toc toc_depth fig_caption true 4 true

Data organization

All material was organized as described in this structure below:

/hihisiv_gitlab/      
|--- a_code/
|    |--- metadata/
|    |--- microarray_analysis/
|    |--- rna-seq_analysis/
|--- b_database/
|    |--- Dockerfile
|    |--- init.sql
|--- c_web_app/
|    |--- hihisiv_webapp/
|--- README.md             
|--- docker-compose.yml
|--- metadata.html

A code

Microarray_analysis

• parameters.R
• dependencies.R
• raw_activity.R (CEL files, normalized matrix - affy, impute)
• e-set_activity.R
• module_processing.R
• limma_activity.R (eSet object and phenodata matrix, differentially expressed genes matrix, limma, ggplot2, RColorBrewer)

Rna-seq_analysis

• get_sra.sh (archive with ids, SRA data, aria2c from aria2)
• sra_to_fastq.sbatch (SRA data, fastq files, fastq-dump from sratoolkit (v. 2.11.3))
• quality_control.sh (fastq, .html reports, fastqc multiqc)
• alignment_rsem.sh (fastq paired, bowtie2; perl; rsem)
• limma_voom.R
• rsem_matrix.sbatch (*genes.results, geneMat.txt, bowtie2; rsem)

B database

Database docker

• a) Build database docker container (remove old containers and images if needed):

cd B_Database/ docker build -t hihisiv-postgres .

• b) Create empty directory on host to store database files, for example:

mkdir /home/user/hihisiv_db

C web_app

• Build web application docker container (remove old containers and images if needed):

cd c_web_app/hihisiv_webapp

docker build -t hihisiv-webapp .

All-in-one - docker-compose

Requirements: docker and docker-composed

Installation steps:

• Edit web application container environment variables to enter database initialization file directory (b_database/tables_hihisiv) and database files directory:

vi .env

• Set VIRTUAL_HOST on docker-compose.yml to host name of the host that will run the web application.

• Start containers with:

docker-compose up -d

• Open on the browser:

localhost

• Stop docker:

docker-compose down