This page was last updated on Sunday, 28-Jun-2015 10:05:34 CDT

Installation notes for MCScanX version Nov. 11, 2013 and MCScanX-transposed version Mar. 28, 2013

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Prerequisites

• Java

Installation

1. $ cd /programinstallers/
2. $ wget -N http://chibba.pgml.uga.edu/mcscan2/MCScanX.zip
3. $ wget -N http://chibba.pgml.uga.edu/mcscan2/transposed/MCScanX-transposed.zip
4. $ cd /usr/local/bin
5. $ unzip /programinstallers/MCScanX.zip
6. $ unzip /programinstallers/MCScanX-transposed.zip
7. $ cd MCScanX
8. $ make
9. 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 scope
   make: *** [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
10. $ make
11. $ cd ../MCScanX-transposed
12. $ make
13. Because there are two different versions of MCScanX in the two directories, nothing is installed to the default PATH
     
14. 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
15. $ git clone https://github.com/wyp1125/MCScanx.git
16. $ cd MCScanx
17. 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
18. $ make
19. Save a bit of space
    $ rm .git -rf