Download and Unpacking
The PEMer package can be dowloaded from PEMer_Package.tgz. To unpack the package, use the following command lines. The software can be obtained freely by non-commercial users (for permissions, see also:
http://www.gersteinlab.org/misc/permissions.html)gunzip PEMer_package.tgz
tar -xvf PEMer_package.tar
Prerequisites and Installation
PEMer workflow:
- Install Python 2 or higher
- Install Perl 5.8 or higher
- Install Megablast software
Free megablast software is included in the blast package which can be obtained from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/
- Install Smith-Waterman best local alignment software
Free Smith-Waterman software is included in the EMBOSS package which can be obtained from http://emboss.sourceforge.net/
SV simulation:
- Install ROOT package
Free ROOT package can be obtained from http://root.cern.ch/
- Compile SV-simulation programs
Type the following:
cd PEMer_Package/SV_simulation/sv_sim
makeIf the compilation fails the most likely reason is that you need to change compiler flags. Please type in the following to get the compiler flags specific to your platform.
root-config --cflags
Please insert the output to the line defining ROOTFLAGS variable in the file ‘Makefile’. Type in 'make clean' and then ‘make’.
BreakDB:
- Install Python 2.3.5
- Install MySQLdb Python Package
Free MySQLdb Python Package can be obtained from http://sourceforge.net/projects/mysql-python
- Install MySQL Database 4.0 or higher
Free MySQL Database can be obtained from http://dev.mysql.com/downloads/
- Install Apache Web server or equivalent
Free Apache HTTP server can be obtained from http://httpd.apache.org/.