title | header-includes | output | ||||||||||||||||||||
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HIHISIV - The database of gene expression in HIV and SIV host immune response |
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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
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)
- 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
- Build web application docker container (remove old containers and images if needed):
cd c_web_app/hihisiv_webapp
docker build -t hihisiv-webapp .
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
ondocker-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