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  • Samtools mac install problems

    Hello - relative bioinformatics newbie here, so apologies in advance if these are stupid questions!

    I'm trying to install Samtools (tried both 1.4.1 and 1.5) on Mac OS X 10.11.6.

    I seem to get through the install process (using ./configure, make and make install without any error messages, but it seems to me that the resulting Samtools folder only contains a limited selection of the executables that should be available:

    ace2sam* export2sam.pl* maq2sam-short* novo2sam.pl* sam2vcf.pl* seq_cache_populate.pl* wgsim*
    blast2sam.pl* interpolate_sam.pl* md5fa* plot-bamstats* samtools* soap2sam.pl* wgsim_eval.pl*
    bowtie2sam.pl* maq2sam-long* md5sum-lite* psl2sam.pl* samtools.pl* varfilter.py* zoom2sam.pl*

    For example, faidx is not there. Am I missing something here - is there another folder with the rest of the executables?

    Thanks in advance!

  • #2
    I answered your identical question on Biostars: https://www.biostars.org/p/258576/ already.

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