01. Requirements

Requirements

We make P-CAPS for end users who deal with bioinformatics for their experiments. If you have any problem about running tools, this server will help you can run tools much easier than before. Before start this server with shiny, check these requirements below.

1. This code is optimized to LINUX system and bash shell.
2. Install shiny server to system where you want to launch P-CAPS.
   Shiny server : https://www.rstudio.com/products/shiny/download-server/
   Because our code contact to your server and run on your LINUX system.
3. We develop this server for academic use. Because some tools can use in academic part, Please do not use our source code for commercial works.
4. Install needed tools for running P-CAPS server.

   • Tool list

     • RNAmmer - Finding rRNA region (Academic use)
       http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
     • tRNAscan-SE - Finding tRNA region
       http://lowelab.ucsc.edu/tRNAscan-SE/
     • Prodigal - Gene prediction
       http://prodigal.ornl.gov/
     • GenemarkS - Gene prediction (Academic use)
       http://exon.gatech.edu/Genemark/index.html
     • Blastp(DB:Uniref90) - Protein naming using by protein DB
       https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
       • Uniref90 : http://www.uniprot.org/downloads
     • InterProScan - Protein domain analysis
       https://www.ebi.ac.uk/interpro/download.html
       • Pfam : http://pfam.xfam.org/
       • Phobius : http://phobius.sbc.su.se/ (Academic use)
       • TMHMM : http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm (Academic use)
       • SignalP : http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp (Academic use)
     • BUSCO - Genome completeness test
       http://busco.ezlab.org/
     • JBrowse - Annotation result visualization
       http://jbrowse.org/