This page was last updated on Thursday, 14-Jan-2016 16:52:56 CST

Installation notes for fastQValidator version 0.1.1a

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Prerequisites

None

Installation

1. $ ver="0.1.1a"
2. $ cd /programinstallers/
3. $ wget -N http://genome.sph.umich.edu/w/images/2/20/FastQValidatorLibStatGen.$ver.tgz
4. $ tar -zxvf FastQValidatorLibStatGen.$ver.tgz
5. $ cd fastQValidator_$ver
6. $ make
   …

   In file included from GenomeSequence.h:47:0,
                    from Chromosome.h:4,
                    from Chromosome.cpp:2:
   GenomeSequenceHelpers.h: In member function ‘void ChromosomeInfo::setSpecies(const char*)’:
   GenomeSequenceHelpers.h:67:44: error: argument to ‘sizeof’ in ‘char* strncpy(char*, const char*, size_t)’ call is the same expression as the source; did you mean to provide an explicit length? [-Werror=sizeof-pointer-memaccess]
            strncpy(species, newSpecies, sizeof(newSpecies));
                                               ^
   cc1plus: all warnings being treated as errors
   make[2]: *** [obj/Chromosome.o] Error 1
   make[2]: Leaving directory `/programinstallers/fastQValidator_0.1.1a/libStatGen/general'

   …
7. Although this points right to the error, there are others. We need an up to date version of libStatGen.
   $ rm libStatGen -rf
8. $ git clone git://github.com/statgen/libStatGen.git
9. $ make
10. Manual install
    $ cp -puv fastQValidator/bin/fastQValidator /usr/local/bin/
11. Cleanup
    $ cd .. && rm fastQValidator_$ver -rf