![]() ![]() ![]() If you need some environment variables, you can set them for a one-off run of the command: $ CFLAGS=. The cpan command took care of dependencies too, so it also installed BioPerl for me. There were some compiler warnings, but the module passed its tests and installed. I then installed Bio::DB::Sam: $ cpan Bio::DB::Sam From your question, I don't think you had a problem here. There were some warnings, but it appears to work. You don't need it for the rest of BioPerl, so it's not a hard dependency.įor Bio::DB::Sam, you need samtools-0.1.17 (the latest version the module works with according to its docs). That's what the The optional module Bio::DB::Sam message is about. You need to install an additional (optional) module to use samtools. This is a good idea because using /usr/bin/perl requires sudo, it involves messing with the system libraries which might cause an issue, and the recent Apple changes mean that working with root directories/libraries is completely unstable. That will give you a kick-ass Perl with some nice features not available with your "system" Perl. Something along the lines of: curl -L | bash That might sound challenging but it is just a few commands. That would be my first step: set up perlbrew, install Perl 5.22, then install cpanminus. Other people may have their preferred method, but perlbrew (combined with cpanminus) will make this type of work fun and much less of a pain (and they are popular choices). You find it easier to manage Perl without using the "system" Perl, and here is one solution. ![]() That is my opinion and a word of caution though, nothing wrong with Bio::DB::Sam. This is really what you should be using because the version of SAMtools mentioned above is really old and not being developed. I don't know what you are trying to do but I will mention that the fine folks over at EBI have developed bindings to htslib called Bio::DB::HTS based on Lincoln Stein's XS code in the Bio::DB::Sam module. That should get you a working Bio::DB::Sam. It is required on Linux, and since the module uses so much memory you will likely only be using this on a Linux machine. Note, the extra CFLAGS argument may not be needed on your Mac, so try without it first. The last command will allow you to install the Perl module without looking for the PATH to samtools and being prompted for it. ![]() I previously provided a solution to do this and I'll show a better way here (just use a package manager for the Perl module). This is an important point because you may run into issues using SAM/BAM files generated with samtools or other aligners because most tools use htslib these days.įor building the module, you are on the right track with the version you are using but it is difficult to build if you do not know the correct flags. The module Bio::DB::Sam provides bindings to an older version of samtools that did not rely htslib.
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