prokka-software
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prokka-software [2020/05/17 13:12] – 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: |
< | < | ||
Line 19: | Line 19: | ||
< | < | ||
$ prokka</ | $ prokka</ | ||
+ | |||
+ | **Note:** Please use the %%'' | ||
===== Installation ====== | ===== Installation ====== | ||
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< | < | ||
- | $ git clone https:// | + | $ wget https:// |
- | $ cd prokka | + | $ tar xf v1.14.6.tar.gz |
- | $ git checkout | + | $ 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:: | ||
Line 34: | Line 35: | ||
$ grep -rh -oE "use Bio:: | $ grep -rh -oE "use Bio:: | ||
$ cpanm -l perl5 Bio:: | $ cpanm -l perl5 Bio:: | ||
+ | # we apparently also need 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 " | ||
- | *Note:* You can try without | + | **Note 2:** You can try without |
prokka-software.1589721130.txt.gz · Last modified: 2020/05/17 13:12 by aorth