SetupMeFirst.sh

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######## Welcome, thank you for downloading Genome Chronicler, let's do some initial setup ########

### Download reference data
wget --http-user=blicp --http-password=bpublicdata http://genomicsdata.cs.ucl.ac.uk/blic_public/afonso/PGPUK/reference.tar.gz

### Uncompress reference data
tar xvf reference.tar.gz
rm -rf reference.tar.gz

### Download some needed binaries
wget --http-user=blicp --http-password=bpublicdata http://genomicsdata.cs.ucl.ac.uk/blic_public/afonso/PGPUK/software.tar.gz

### Uncompress software folders
tar xvf software.tar.gz
rm -rf software.tar.gz

### Setup symlinks for software (change this to softare.darwin if you are running this on a mac)
ln -sf software.linux software
#ln -sf software.darwin software

### Download test data?
#wget --http-user=blicp --http-password=bpublicdata http://genomicsdata.cs.ucl.ac.uk/blic_public/afonso/PGPUK/testData.tar

### Uncompress test data
#tar xvf testData.tar 
#rm -rf testData.tar 

### Run initial test to check for further problems and unmet dependencies
#time perl GenomeChronicler_mainDruid.pl --bamFile=testData/tester_1_GRCh38.bam --vepFile=testData/tester_1_VEP.html


### Other deps

# # R
#TeachingDemos package
#RColorBrewer package

# # perl
#cpan File::chdir
#cpan Config::General
#cpan Data::Dumper
#cpan Excel::Writer::XLSX
#cpan DBI
#cpan DBD::SQLite

# # LaTeX
# booktabs
# calc
# fullpage
# csvsimple
# fancyhdr
# lastpage
# inputenc
# fontenc
# longtable
# multicol
# xcolor
# tikz
# hyperref