Created basic website structure and added deployment script

# coronavirus

# Coronavirus student project

A PB051 bioinformatics project at the Faculty of Informatics at MU in Brno.

### Goals (with web pages to create):

1. Collect as many coronavirus sequences as possible (Page 1 - Sequence data)

1. Using HMMER create a profile-HMM of coronavirus sequence and/or its important subsequences (Page 2 - HMM Alignment)

1. Find other related sequences in public sequence databases (Page 3 - Related sequences)

1. Create a labeled phylogenetic tree of the aligned sequences (Page 4 - Phylogenetic trees)

1. Phylogeographic analysis (Page 5 - Phylogeography)

1. Time series analysis (Page 6 - Time series) 

## Sources of relevant data

[NCBI: SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences](https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/)

## References

[Wikipedia background information](https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2)

[Cohen (2020): Mining coronavirus genomes for clues to the outbreak’s origins](https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins)

[Data integration, manipulation and visualization of phylogenetic trees](https://yulab-smu.github.io/treedata-book/)

# Specify server:path (in scp format) to where the coronavirus site is being deployed using $1 bash variable

# Example: 

# ./deploy.sh lexa@helix.fi.muni.cz:/mnt/lexa/public_html/coronavirus

# Note:

# To deploy up-to-date static webpages, run RMarkdown render_site() command in R first

#cp *.html /mnt/lexa/public_html/pa055/.

#cp -R images /mnt/lexa/public_html/pa055/.