Elementolab/ChIPseeqer Install old

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Elementolab/

INSTALLATION INSTRUCTIONS

• 1) Download the source code using our SVN repository Subversion

svn checkout --username guest --password email@email.com https://pbtech-vc.med.cornell.edu/public/svn/elementolab/ChIPseeqer/trunk ChIPseeqer/

(note: guests SVN users cannot commit any changes; please use your PBtech identifiers if you need to make changes to the code)

• 2) Change directory using:

cd ChIPseeqer

• 3) Read the LICENSE file. It basically says that you can (almost) do whatever you want with the code and program, provided you accept that we cannot be held liable if anything bad happens. If you have not read the LICENSE file, or do not accept the terms, please do not use ChIPseeqer.

• 4) If not already installed, install the PERL compatible regular expression module (PCRE) from http://www.pcre.org/. Follow the instructions, compile and install the library. (http://jones.ling.indiana.edu/wiki/How_to_install_PCRE)

You can also do this using macports:

 sudo port install pcre

There are a few more modules that may need to be installed, e.g. the IO::Zlib PERL module. It is also quite possible you would have to install the libz library (http://www.zlib.net/)

• 5) Compile ChIPseeqer using:

make

(if you see an error message about -arch x86_64, try: make -f Makefile.linux instead of make)

• 6) Set the CHIPSEEQERDIR environment variable

Read How to set the CHIPSEEQERDIR variable

• 7) Optional: some of the programs require additional installation steps. For example, to use Elementolab/ChIPseeqerFindPeaksWithMotifMatch, you will need to perform the following steps:

svn checkout --username guest --password email@email.com https://pbtech-vc.med.cornell.edu/public/svn/elementolab/MYSCANACE/trunk MYSCANACE/
svn checkout --username guest --password email@email.com https://pbtech-vc.med.cornell.edu/public/svn/elementolab/BIO-C/trunk BIO-C/
cd MYSCANACE
make
export MYSCANACEDIR=/path/to/MYSCANACE  # try export MYSCANACEDIR=`pwd`