Hi Nicola,
I'm going to cc this to the GBrowse mailing list, since there are lots of people experienced with compiling SAMtools. The reason I don't personally know much about compiling it is that when I use Ubuntu, I just use apt-get to install it:
sudo apt-get install libbio-samtools libbio-samtools-perl That installs SAMtools 1.18 and Bio::DB::Sam 1.32. Scott On Mon, Oct 7, 2013 at 8:28 AM, Nicola Losito <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Hi Nicola, Please keep the GBrowse mailing list cc'ed so the discussion can be archived and searchable. I got the name wrong on the first package; checking:
sudo apt-cache search samtools yeilds libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files maq - maps short fixed-length polymorphic DNA sequence reads to reference sequences
samtools - processing sequence alignments in SAM and BAM formats so the one you needed was "samtools". In fact, since it is a prerequisite for libbio-samtools-perl, and that successfully installed, you already have samtools installed via apt-get.
Scott On Mon, Oct 7, 2013 at 10:55 AM, Nicola Losito <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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