prokka-software
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
prokka-software [2017/02/20 11:19] – created joguya | prokka-software [2023/08/09 06:46] (current) – aorth | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== | + | ====== |
+ | |||
+ | 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 ===== | ||
- | See which versions | + | See which versions are available: |
< | < | ||
- | Load prokka | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ prokka</ | ||
+ | |||
+ | **Note:** Please use the %%'' | ||
===== Installation ====== | ===== Installation ====== | ||
Line 21: | Line 26: | ||
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/5.22.3 | + | $ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module:: |
- | $ cpanm SWISS::Entry SWISS::KW XML::Simple | + | $ export PERL5LIB=perl5/lib/perl5 |
- | $ sed -i 's#/usr/bin/perl.*#/usr/bin/env perl#' bin/* | + | $ grep -rh -oE "use Bio::.*$" bin/* binaries/* | sort -u | awk ' |
- | $ sudo mkdir -p / | + | $ cpanm -l perl5 Bio::AlignIO Bio::Root::Version Bio:: |
- | $ sudo cp -rv . / | + | # we apparently also need Bio:: |
- | </ | + | $ cpanm -l perl5 Bio:: |
+ | $ ./ | ||
+ | # Upgrade tbl2asn, see: https://github.com/tseemann/ | ||
+ | $ wget https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/ | ||
+ | $ gunzip | ||
+ | $ chmod +x linux64.tbl2asn | ||
+ | $ mv linux64.tbl2asn binaries/ | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo cp -r . / | ||
+ | |||
+ | **Note 1:** Prokka only says that it requires " | ||
+ | **Note 2:** You can try without %%'' |
prokka-software.1487589554.txt.gz · Last modified: 2017/02/20 11:19 by joguya