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sestaton / tephra

A tool for discovering transposable elements and describing patterns of genome evolution
MIT License
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Problems running #30

Closed juancresc closed 6 years ago

juancresc commented 6 years ago

Installed everything as required (and a few more perl libs) and now I get the following. Seems like a problem with Bio/DB/HTS specifically, I installed htslib as required and the module manually.

tephra all -c tephra_config.yml Can't load '/usr/local/lib/x86_64-linux-gnu/perl/5.22.1/auto/Bio/DB/HTS/HTS.so' for module Bio::DB::HTS: libhts.so.2: cannot open shared object file: No such file or directory at /usr/lib/x86_64-linux-gnu/perl/5.22/DynaLoader.pm line 187. at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71. Compilation failed in require at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71. BEGIN failed--compilation aborted at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Bio/DB/HTS/Kseq.pm line 71. Compilation failed in require at /usr/local/share/perl/5.22.1/Tephra/Stats/Age.pm line 17. BEGIN failed--compilation aborted at /usr/local/share/perl/5.22.1/Tephra/Stats/Age.pm line 17. Compilation failed in require at /usr/local/share/perl/5.22.1/Tephra/Command/age.pm line 11. BEGIN failed--compilation aborted at /usr/local/share/perl/5.22.1/Tephra/Command/age.pm line 11. Compilation failed in require at /usr/local/share/perl/5.22.1/App/Cmd.pm line 194. App::Cmd::_command("Tephra", HASH(0x1374f30)) called at /usr/local/share/perl/5.22.1/App/Cmd.pm line 171 App::Cmd::new("Tephra", HASH(0x1374f30)) called at /usr/local/bin/tephra

sestaton commented 6 years ago

Can you share the commands you used to install? That would help diagnose the issue.

Thanks.

juancresc commented 6 years ago

The issue was because I installed htslib 1.9 and 1.6, but 1.5 was required for Bio::DB::HTS-

wget https://github.com/samtools/htslib/archive/1.5.zip
unzip 1.5.zip
cd htslib-1.5/
sudo make install
ldconfig

and then cpan Bio::DB::HTS

sestaton commented 6 years ago

Thanks for the feedback. I'm using an earlier version of htslib (v1.3.1), but I will test with later versions.

Ideally, I'd suggest using the automated install route because it is tested and will be easier to tune, whereas custom/manual installs are more difficult to debug.