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comparison tool_dependencies.xml @ 3:fffa1ae330ae draft

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Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later).
author crs4
date Mon, 09 Dec 2013 04:58:14 -0500
parents 4bafaa074484
children 5c0030f52b83
comparison
equal deleted inserted replaced
2:4bafaa074484 3:fffa1ae330ae
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="blast+" version="2.2.28"> 3 <package name="blast+" version="2.2.28">
4 <repository changeset_revision="ed85ca8e4295" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="23b9ba41ad00" 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"> 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" /> 13 <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="barrnap" version="0.2"> 15 <package name="gnu_parallel" version="20131122">
16 <repository changeset_revision="8ab7a17861ea" name="package_barrnap_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="infernal" version="1.1rc4"> 18 <package name="barrnap" version="0.3">
19 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 19 <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
20 </package>
21 <package name="infernal" version="1.1">
22 <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
20 </package> 23 </package>
21 <package name="prokka" version="1.7"> 24 <package name="prokka" version="1.7">
22 <install version="1.0"> 25 <install version="1.0">
23 <actions> 26 <actions>
24 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> 27 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
27 <destination_directory>$INSTALL_DIR</destination_directory> 30 <destination_directory>$INSTALL_DIR</destination_directory>
28 </action> 31 </action>
29 <action type="set_environment"> 32 <action type="set_environment">
30 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
31 </action> 34 </action>
32 <action type="set_environment">
33 <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable>
34 </action>
35 </actions> 35 </actions>
36 </install> 36 </install>
37 <readme> 37 <readme>
38 Warning: Prokka includes custom databases and is thus about a 2.0 GB download! 38 Warning: Prokka includes custom databases and is thus about a 2.0 GB download!
39 39
40 Dependencies of Prokka which needs to be installed separately: 40 Dependencies of Prokka which needs to be installed separately:
41 - 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;
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/ ); 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/ );
43 - Prodigal ( http://prodigal.ornl.gov/ ) &gt;= 2.60 ; 43 - 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 ;
45 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20130422 ;
46 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 .
47 44
48 Configuration: Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus). 45 Configuration: Previously (until Release 2), the PROKKA_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of CPUs to use (--cpus). This is not used anymore and may be removed.
49 </readme> 46 </readme>
50 </package> 47 </package>
51 </tool_dependency> 48 </tool_dependency>