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comparison tool_dependencies.xml @ 6:3ad7ef0ba385 draft

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Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
author crs4
date Mon, 27 Oct 2014 06:45:52 -0400
parents b9fea998270a
children f5e44aad6498
comparison
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5:b9fea998270a 6:3ad7ef0ba385
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="23b9ba41ad00" 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="https://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="https://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="https://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="https://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="tbl2asn" version="22.4"> 15 <package name="tbl2asn" version="23.7">
16 <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="gnu_parallel" version="20131122"> 18 <package name="gnu_parallel" version="20131122">
19 <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 19 <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
20 </package> 20 </package>
21 <package name="barrnap" version="0.3"> 21 <package name="barrnap" version="0.5">
22 <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 22 <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
23 </package> 23 </package>
24 <package name="infernal" version="1.1"> 24 <package name="infernal" version="1.1">
25 <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 25 <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
26 </package> 26 </package>
27 <package name="minced" version="0.1.4"> 27 <package name="minced" version="0.1.6">
28 <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 28 <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
29 </package> 29 </package>
30 <package name="prokka" version="1.8"> 30 <package name="prokka" version="1.10">
31 <install version="1.0"> 31 <install version="1.0">
32 <actions> 32 <actions>
33 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> 33 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
34 <action target_filename="bin/prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action> 34 <action type="shell_command">bin/prokka --setupdb</action>
35 <action type="move_directory_files"> 35 <action type="move_directory_files">
36 <source_directory>.</source_directory> 36 <source_directory>.</source_directory>
37 <destination_directory>$INSTALL_DIR</destination_directory> 37 <destination_directory>$INSTALL_DIR</destination_directory>
38 </action> 38 </action>
39 <action type="set_environment"> 39 <action type="set_environment">
40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
41 </action> 41 </action>
42 </actions> 42 </actions>
43 </install> 43 </install>
44 <readme> 44 <readme>
45 Warning: Prokka includes custom databases and is thus about a 2.0 GB download! 45 Warning: Prokka includes custom databases and is thus about a 340 MB download!
46 46
47 Dependencies of Prokka which needs to be installed separately: 47 Dependencies of Prokka which needs to be installed separately:
48 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; 48 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
49 - 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/ ). 49 - 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/ ).
50 50