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comparison tool_dependencies.xml @ 2:4bafaa074484 draft

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Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
author crs4
date Fri, 25 Oct 2013 08:59:51 -0400
parents 4b6f16a79fe4
children fffa1ae330ae
comparison
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1:4b6f16a79fe4 2:4bafaa074484
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="blast+" version="2.2.26+"> 3 <package name="blast+" version="2.2.28">
4 <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="ed85ca8e4295" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="hmmer" version="3.1b1"> 6 <package name="hmmer" version="3.1b1">
7 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="aragorn" version="1.2.36"> 9 <package name="aragorn" version="1.2.36">
10 <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="prodigal" version="2.60">
13 <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="barrnap" version="0.2">
16 <repository changeset_revision="8ab7a17861ea" name="package_barrnap_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
17 </package>
12 <package name="infernal" version="1.1rc4"> 18 <package name="infernal" version="1.1rc4">
13 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 19 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package> 20 </package>
15 <package name="prokka" version="1.7"> 21 <package name="prokka" version="1.7">
16 <install version="1.0"> 22 <install version="1.0">
17 <actions> 23 <actions>
18 <action target_filename="" type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> 24 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
19 <action type="move_directory_files"> 25 <action type="move_directory_files">
20 <source_directory>.</source_directory> 26 <source_directory>.</source_directory>
21 <destination_directory>$INSTALL_DIR</destination_directory> 27 <destination_directory>$INSTALL_DIR</destination_directory>
22 </action> 28 </action>
23 <action type="set_environment"> 29 <action type="set_environment">
27 <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable> 33 <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable>
28 </action> 34 </action>
29 </actions> 35 </actions>
30 </install> 36 </install>
31 <readme> 37 <readme>
38 Warning: Prokka includes custom databases and is thus about a 2.0 GB download!
39
32 Dependencies of Prokka which needs to be installed separately: 40 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; 41 - 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;= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ); 42 - 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 ; 43 - Prodigal ( http://prodigal.ornl.gov/ ) &gt;= 2.60 ;
36 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ; 44 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ;
37 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ; 45 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ;
38 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 . 46 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 .
39 47
40 Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus). 48 Configuration: Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).
41
42 Note: Prokka is about a 2.0 GB download due to included custom databases.
43 </readme> 49 </readme>
44 </package> 50 </package>
45 </tool_dependency> 51 </tool_dependency>