Requirements

Although EUPAN toolkit integrates more than 10 software, most of these software can be provided to the main program when the specific tool is selected. It is convenient for users to work on supercomputers or clusters. To run the main program of EUPAN toolkit, you only need several software and packages.

1. R 3.1 or later

R is utilized for visulization and statistical tests in EUPAN toolkit. Please install R first and make sure R and Rscript are under your PATH.

Download R here.

2. R packages

Several R packages are needed including ggplot2, reshape2 and ape packages. Follow the Installation step 3 or you can install the packages by yourself.

3. Perl
4. g++
5. Python 2.5, 2.6 or 2.7 (required by QUAST)

Installation procedures

1. Download the EUPAN toolkit here.

2. Uncompress the EUPAN toolkit package.

   tar zxvf EUPAN-vXX.XX.tar.gz

3. Install necessary R packages.

   cd EUPAN-vXX.XX
   Rscript installRPac

4. Compile the source codes.

   make

   You will find executable files: ccov and bam2cov in bin/ directory.

5. Add bin/ to PATH and add lib/ to LD_LIBRARY_PATH.

   To do this, edit your path in the following text and add the text to the end of the file ~/.bash_profile

   export PATH=$PATH:/path/to/EUPAN/bin:
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/EUPAN/lib/:
   export PERL5LIB=$PERL5LIB:/path/to/EUPAN/lib/:
   source /path/to/EUPAN/bin/eupan_cmd.sh

   and run

   source ~/.bash_profile

6. Test if EUPAN toolkit is installed successfully

   eupan

   If you could see the following content, congratulations! EUPAN toolkit is successfully installed. If not, see if all the requirements are satisfied; or you may contact the authors for help.

   Usage: eupan <command> ...
   
   Avalable commands:
           qualSta         View the overall sequencing quality of a large number of files
           trim            Trim or filter low-quality reads parallelly
           alignRead       Map reads to a reference parallelly
           sam2bam         Covert alignments (.sam) to sorted .bam files
           bamSta          Statistics of parallel mapping
           assemble        Assemble reads parallelly
           assemSta        Statistics of parallel assembly
           getUnalnCtg     Extract the unaligned contigs from nucmer alignment (processed by quast)
           rmRedundant     Remove redundant contigs of a fasta file
           pTpG            Get the longest transcripts to represent genes
           geneCov         Calculate gene body coverage and CDS coverage
           geneExist       Determine gene presence-absence based on gene body coverage and CDS coverage
           subSample       Select subset of samples from gene PAV profile
           gFamExist       Determine gene family presence-absence based on gene presence-absence
           bam2bed         Calculate genome region presence-absence from .bam
           fastaSta        Calculate statistics of fasta file
           sim             simulation and plot of the pan-genome and the core genome