Differences

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--- prokka-software [2022/06/30 17:42] – aorth
+++ prokka-software [2023/08/09 06:46] (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 38: / 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.