Perform a PEFF test under Windows:
(This requires that Perl is installed. Perhaps Strawberry Perl: http://strawberryperl.com/ or some other version)

#### Check HOMEPATH and set the location of the Proteomics::PEFF distribution
echo %HOMEPATH%
  (if this is not set to something sensible, that replace %HOMEPATH% below with C:\Users\myusername or something like that)
cd %HOMEPATH%
set PEFF=%HOMEPATH%\Documents\ProteomicsPEFF
mkdir %PEFF%

#### Download the Proteomics::PEFF distribution
cd %PEFF%
wget http://www.peptideatlas.org/export/PEFF/ProteomicsPEFF.zip
  (or alternatively, manually download the zip file at that URL and save it to %PEFF%
unzip ProteomicsPEFF.zip
  (or unzip with Windows Explorer)

#### If okay, add the bin area to the PATH and set the testData location
set PATH=%PEFF%\bin\PEFF;%PATH%
set PEFFTEST=%PEFF%\testData\PEFF

#### Test the configuration. If this doesn't work, troubleshoot before proceeding
perl %PEFF%/bin/testConfig.pl

#### Test the validator on some files. The first 3 should produce no errors.
#### The fourth should spew lots of errors because the file is NOT valid
validatePEFF --input %PEFFTEST%/PEFF_Minimal_Valid.peff
validatePEFF --input %PEFFTEST%/PEFF_AnnotID_Insulin_Valid.peff
validatePEFF --input %PEFFTEST%/crap.peff
validatePEFF --input %PEFFTEST%/PEFF_Tiny_INValid1.peff

#### In a test directory, create a PEFF file from crap.fasta, applying (di+)methyl to TRYP lysines
cd %HOMEPATH%
mkdir testPEFF
cd testPEFF
copy %PEFFTEST%\crap.fasta .
copy %PEFFTEST%\crap.fasta.header .
copy %PEFFTEST%\crap_alterations.txt .

alterPEFF --operation convertFASTAToPEFF --input crap.fasta --output crap.peff --databaseMetadataFile crap.fasta.header --alterations crap_alterations.txt --verbose 1