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view pyPRADA_1.2/tools/samtools-0.1.16/INSTALL @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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System Requirements =================== SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA file. SAMtools' faidx is able to index a razip-compressed FASTA file to save diskspace. Older zlib also works with SAMtools, but razip cannot be compiled. The text-based viewer (tview) requires the GNU ncurses library <http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of the modern Linux/Unix distributions. If you do not have this library installed, you can still compile the rest of SAMtools by manually changing: `-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and comment out the line starting with `LIBCURSES='. Compilation =========== Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile razip with `make razip'. Installation ============ Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to a location you want (e.g. a directory in your $PATH). You may also copy `samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such that the `man' command may find the manual.