Differences

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--- prokka-software [2022/06/30 09:57] – aorth
+++ prokka-software [2025/05/07 12:42] (current) – aorth
@@ Line 13: / Line 13: @@
 ===== Usage =====
-See which versions of Prokka are available:
+See which versions are available:
 <code>$ module avail prokka</code>
@@ Line 30: / Line 30: @@
 $ tar xf v1.14.6.tar.gz
 $ cd prokka-1.14.6
-$ module load perl/5.28.2
 $ mkdir perl5
 $ cpanm -l perl5 Time::Piece XML::Simple Digest::MD5 Module::Build
@@ Line 39: / Line 38: @@
 $ cpanm -l perl5 Bio::SearchIO::hmmer3 --force
 $ ./bin/prokka --setupdb
+# Upgrade tbl2asn, see: https://github.com/tseemann/prokka/issues/511
+$ wget https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
+$ gunzip  linux64.tbl2asn.gz
+$ chmod +x linux64.tbl2asn
+$ mv linux64.tbl2asn binaries/linux/tbl2asn
 $ sudo mkdir -p /export/apps/prokka/1.14.6
-$ sudo cp -r . /export/apps/prokka/1.14.6
+$ sudo cp -r . /export/apps/prokka/1.14.6</code>
-</code>
 **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 "use" statements.
 **Note 2:** You can try without %%''--force''%% if you want, but many Perl modules "bail out" during installation because one out of a few hundred (or thousand) obscure or comprehensive tests fail.
+**Note 3:** As of 2025 ''tbl2asn'' is discontinued and you need to hack it with ''https://github.com/rpetit3/tbl2asn-forever'' which uses faketime to pretend it is 2019