Installation notes for MCScanX version

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Installation notes for MCScanX version

Prerequisites

Java

Installation

$ cd /programinstallers/
$ wget -N http://chibba.pgml.uga.edu/mcscan2/MCScanX.zip
$ wget -N http://chibba.pgml.uga.edu/mcscan2/transposed/MCScanX-transposed.zip
$ cd /usr/local/bin
$ unzip /programinstallers/MCScanX.zip
$ unzip /programinstallers/MCScanX-transposed.zip
$ cd MCScanX
$ make

Only if the following error occurs during make

g++ struct.cc mcscan.cc read_data.cc out_utils.cc dagchainer.cc msa.cc permutatio$msa.cc: In function ‘void msa_main(const char*)’:msa.cc:289:22: error: ‘chdir’ was not declared in this scopemake: *** [mcscanx] Error 1

then for each of the following files:

msa.h dissect_multiple_alignment.h detect_collinear_tandem_arrays.h

Edit them by adding #include <unistd.h> before the first line

 for f in msa.h dissect_multiple_alignment.h detect_collinear_tandem_arrays.h ; do sed -i ‘1 i\#include <unistd.h>’ $f ; done

$ make
$ cd ../MCScanX-transposed
$ make
Because there are two different versions of MCScanX in the two directories, nothing is installed to the default PATH
There is a different version called MCScanx (note lower case x) last updated Sept. 13, 2011 (commit 3b2f1a5d0e) at https://github.com/wyp1125/MCScanx.
One nice addition to this version is that it has error checking to make sure that the input files exist!
There is some confusing documentation about bed instead of gff input, but the code has no handler for bed files it appears.
To install this version
$ cd /usr/local/bin
$ git clone https://github.com/wyp1125/MCScanx.git
$ cd MCScanx

Same problem as above fixed by

for f in msa.h dissect_multiple_alignment.h detect_syntenic_tandem_arrays.h ; do sed -i ‘1 i\#include <unistd.h>’ $f ; done

$ make
Save a bit of space
$ rm .git -rf

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