prokka-software
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prokka-software [2017/02/20 11:19] – created joguya | prokka-software [2022/06/30 17:42] – aorth | ||
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- | ====== | + | ====== |
+ | |||
+ | Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. | ||
- | Prokka is a software tool for the rapid annotation of prokaryotic genomes. | ||
===== Information ===== | ===== Information ===== | ||
- | * Version: 1.11 | + | * Version: 1.14.6 |
* Added: February, 2017 | * Added: February, 2017 | ||
- | * Link: http://www.vicbioinformatics.com/software.prokka.shtml | + | |
+ | | ||
===== Usage ===== | ===== Usage ===== | ||
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< | < | ||
- | Load prokka | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ prokka</ | ||
+ | |||
+ | **Note:** Please use the %%'' | ||
===== Installation ====== | ===== Installation ====== | ||
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Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ cd /tmp/ | + | $ wget https:// |
- | $ wget -qO- https:// | + | $ tar xf v1.14.6.tar.gz |
- | $ cd prokka-1.11/ | + | $ cd prokka-1.14.6 |
- | $ scl enable devtoolset-3 bash | + | $ mkdir perl5 |
- | $ module load perl/ | + | $ cpanm -l perl5 Time::Piece XML:: |
- | $ cpanm SWISS:: | + | $ export PERL5LIB=perl5/lib/perl5 |
- | $ sed -i 's#/usr/bin/perl.*#/usr/bin/env perl#' bin/* | + | $ grep -rh -oE "use Bio:: |
- | $ sudo mkdir -p / | + | $ cpanm -l perl5 Bio:: |
- | $ sudo cp -rv . / | + | # we apparently also need Bio:: |
+ | $ cpanm -l perl5 Bio:: | ||
+ | $ ./bin/prokka --setupdb | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo cp -r . / | ||
</ | </ | ||
+ | **Note 1:** Prokka only says that it requires " | ||
+ | |||
+ | **Note 2:** You can try without %%'' |
prokka-software.txt · Last modified: 2023/08/09 06:46 by aorth