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comparison tool_dependencies.xml @ 4:5c0030f52b83 draft

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Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation.
author crs4
date Wed, 08 Jan 2014 04:29:37 -0500
parents fffa1ae330ae
children b9fea998270a
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3:fffa1ae330ae 4:5c0030f52b83
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="tbl2asn" version="22.4">
16 <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
17 </package>
15 <package name="gnu_parallel" version="20131122"> 18 <package name="gnu_parallel" version="20131122">
16 <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="http://toolshed.g2.bx.psu.edu" />
17 </package> 20 </package>
18 <package name="barrnap" version="0.3"> 21 <package name="barrnap" version="0.3">
19 <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> 22 <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
20 </package> 23 </package>
21 <package name="infernal" version="1.1"> 24 <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" /> 25 <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
23 </package> 26 </package>
24 <package name="prokka" version="1.7"> 27 <package name="minced" version="0.1.4">
28 <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
29 </package>
30 <package name="prokka" version="1.8">
25 <install version="1.0"> 31 <install version="1.0">
26 <actions> 32 <actions>
27 <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-1.7.tar.gz</action>
34 <action target_filename="prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action>
28 <action type="move_directory_files"> 35 <action type="move_directory_files">
29 <source_directory>.</source_directory> 36 <source_directory>.</source_directory>
30 <destination_directory>$INSTALL_DIR</destination_directory> 37 <destination_directory>$INSTALL_DIR</destination_directory>
31 </action> 38 </action>
32 <action type="set_environment"> 39 <action type="set_environment">
37 <readme> 44 <readme>
38 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 2.0 GB download!
39 46
40 Dependencies of Prokka which needs to be installed separately: 47 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; 48 - 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/ ); 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/ ).
43 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 .
44 50
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. 51 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.
46 </readme> 52 </readme>
47 </package> 53 </package>
48 </tool_dependency> 54 </tool_dependency>