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--- prokka-software [2020/05/17 13:18]
aorth
+++ prokka-software [2020/09/18 11:47] (current)
aorth
@@ Line 19: / Line 19: @@
 <code>$ module load prokka/1.14.6
 $ prokka</code>
+**Note:** Please use the %%''--cpus''%% option to tell prokka how many CPUs it should use or else it will automatically use eight (8). This number should match the number of CPUs you requested in your SLURM batch allocation.
 ===== Installation ======
@@ Line 34: / Line 36: @@
 $ grep -rh -oE "use Bio::.*$" bin/* binaries/* | sort -u | awk '{print $2}' | sed 's/;//'
 $ cpanm -l perl5 Bio::AlignIO Bio::Root::Version Bio::SearchIO Bio::Seq Bio::SeqFeature::Generic Bio::SeqIO Bio::Tools::CodonTable Bio::Tools::GFF Bio::Tools::GuessSeqFormat --force
+# we apparently also need Bio::SearchIO::hmmer3, but I only discovered that weeks later after trying to test prokka... hmmmm
+$ cpanm -l perl5 Bio::SearchIO::hmmer3 --force
 $ ./bin/prokka --setupdb
 $ sudo mkdir -p /export/apps/prokka/1.14.6

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