prokka-software
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prokka-software [2020/09/18 11:47] – aorth | prokka-software [2023/08/09 06:46] (current) – aorth | ||
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* Added: February, 2017 | * Added: February, 2017 | ||
* Updated: May, 2020 | * Updated: May, 2020 | ||
- | * Link: http://www.vicbioinformatics.com/software.prokka.shtml | + | * Link: https://github.com/tseemann/prokka |
===== Usage ===== | ===== Usage ===== | ||
- | See which versions | + | See which versions are available: |
< | < | ||
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$ tar xf v1.14.6.tar.gz | $ tar xf v1.14.6.tar.gz | ||
$ cd prokka-1.14.6 | $ cd prokka-1.14.6 | ||
- | $ module load perl/5.28.2 | ||
$ mkdir perl5 | $ mkdir perl5 | ||
$ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module:: | $ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module:: | ||
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$ cpanm -l perl5 Bio:: | $ cpanm -l perl5 Bio:: | ||
$ ./ | $ ./ | ||
+ | # Upgrade tbl2asn, see: https:// | ||
+ | $ wget https:// | ||
+ | $ gunzip | ||
+ | $ chmod +x linux64.tbl2asn | ||
+ | $ mv linux64.tbl2asn binaries/ | ||
$ sudo mkdir -p / | $ sudo mkdir -p / | ||
- | $ sudo cp -r . / | + | $ sudo cp -r . / |
- | </ | + | |
- | **Note 1:** Prokka only says that it requires BioPerl, but the BioPerl distribution frowns upon requiring the entire distribution. Here I have attempted to guess which modules are needed by checking the actual Perl " | + | **Note 1:** Prokka only says that it requires |
**Note 2:** You can try without %%'' | **Note 2:** You can try without %%'' |
prokka-software.1600429651.txt.gz · Last modified: 2020/09/18 11:47 by aorth