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comparison tool_dependencies.xml @ 1:4b6f16a79fe4 draft

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Add txt output file. Use a definition list instead of a block quote in <help>. Correct 2 dependency minimum versions.
author crs4
date Thu, 26 Sep 2013 12:39:52 -0400
parents 95505a9fa26f
children 4bafaa074484
comparison
equal deleted inserted replaced
0:95505a9fa26f 1:4b6f16a79fe4
29 </actions> 29 </actions>
30 </install> 30 </install>
31 <readme> 31 <readme>
32 Dependencies of Prokka which needs to be installed separately: 32 Dependencies of Prokka which needs to be installed separately:
33 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; 33 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
34 - Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) &gt;= 1.6.1, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ); 34 - Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) &gt;= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ );
35 - Prodigal ( http://prodigal.ornl.gov/ ) &gt;= 2.60 ; 35 - Prodigal ( http://prodigal.ornl.gov/ ) &gt;= 2.60 ;
36 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ; 36 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ;
37 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20120322 ; 37 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ;
38 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 . 38 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 .
39 39
40 Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus). 40 Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).
41 41
42 Note: Prokka is about a 2.0 GB download due to included custom databases. 42 Note: Prokka is about a 2.0 GB download due to included custom databases.