hammer/plinkseq-sxsw
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This is the PLINK/SEQ repository, to provide the most current sourcecode for developers of PLINK/SEQ, and additionally for users who are willing to experiment with the new code (i.e. to try out new features not yet in the stable release). Please note that this snapshot comes with absolutly no guarantees as to its stability, completeness or correctness, and without the offer of any support besides the (in flux) notes at: http://atgu.mgh.harvard.edu/plinkseq/whatisnew.shtml If you trying to install PLINK/SEQ from source just to run it, you are almost certainly better off just downloading the source for the latest stable release from the main website download page: http://atgu.mgh.harvard.edu/plinkseq/download.shtml Typical steps for creating all PLINK/Seq components from source, assuming certain dependencies are in place (see PREREQUISITES), are given in the section below. If any step fails, please refer to the more detailed description below and to the main website. -------------------------------------------------------------------------------- ## Obtain source git clone https://bitbucket.org/statgen/plinkseq.git cd plinkseq autoreconf -i ## Make PSEQ (sudo if system-wide installation) ./configure make sudo make install ## Make Rplinkseq (with sudo for system-wide installation) cd R/Rplinkseq autoreconf -i ./configure cd .. sudo R CMD INSTALL Rplinkseq ## Test PSEQ from a command line pseq . version ## Test Rplinkseq from within R library(Rplinkseq) -------------------------------------------------------------------------------- ** PREREQUISITES ** PLINK/SEQ uses GNU Autotools for its build system. This is a suite of tools that generates configuration scripts and Makefiles. Specifically, the following tools are required: -- Autoconf 2.61+ -- Automake 1.10+ -- Libtool 2.2+ Please be sure these tools are set up (running, for example, "autoconf -v" to test your version of Autoconf) before you continue. PLINK/SEQ also requires Google's Protocol Buffers. Please be sure you have protobuf version 2.4.1 installed locally: http://code.google.com/p/protobuf/ ** GETTING THE SOURCE ** To clone this repository, run: git clone https://bitbucket.org/statgen/plinkseq.git [target dir] ** INSTALLATION INSTRUCTIONS ** This repository does not contain configure scripts or Makefiles - rather, it contains the Autotools templates (configure.ac and Makefile.am) that can be used to generate these files. As a developer, you need to generate these files before you can build PLINK/SEQ. Conveniently, this is one command: autoreconf -i This will create a bunch of files, including configure scripts and Makefiles. After this step is complete, you are ready to build - just follow the instructions on the website: http://atgu.mgh.harvard.edu/plinkseq/download.shtml. The configuration option --enable-debug will stop compiler optimizations (making code easier to debug and faster to build) and link pseq as a static binary, without a wrapper shell script. ** Rplinkseq configuration options ** To specify the location of libprotobuf, if it is not visible from a system-wide installation, you can pass configure arguments with --configure-args. Also, the --library argument can specify where the library is installed. For example: R CMD INSTALL Rplinkseq --library=/path/to/R/lib/loc --configure-args=--with-protobuf=/path/to/protobuf/
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A version of PLINK/SEQ that will build with Protocol Buffers 2.4.1
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