| Previous changeset 3:fffa1ae330ae (2013-12-09) Next changeset 5:b9fea998270a (2014-01-09) |
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Commit message:
Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation. |
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modified:
prokka.xml readme.rst tool_dependencies.xml |
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| diff -r fffa1ae330ae -r 5c0030f52b83 prokka.xml --- a/prokka.xml Mon Dec 09 04:58:14 2013 -0500 +++ b/prokka.xml Wed Jan 08 04:29:37 2014 -0500 |
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| @@ -1,15 +1,16 @@ -<tool id="prokka" name="Prokka" version="1.2.0"> +<tool id="prokka" name="Prokka" version="1.3.0"> <description>prokaryotic genome annotation</description> <requirements> <requirement type="package" version="2.2.28">blast+</requirement> <requirement type="package" version="3.1b1">hmmer</requirement> <requirement type="package" version="1.2.36">aragorn</requirement> <requirement type="package" version="2.60">prodigal</requirement> - <requirement type="binary">tbl2asn</requirement> + <requirement type="package" version="22.4">tbl2asn</requirement> <requirement type="package" version="20131122">gnu_parallel</requirement> <requirement type="package" version="0.3">barrnap</requirement> <requirement type="package" version="1.1">infernal</requirement> - <requirement type="package" version="1.7">prokka</requirement> + <requirement type="package" version="0.1.4">minced</requirement> + <requirement type="package" version="1.8">prokka</requirement> </requirements> <version_command>prokka --version</version_command> <command> @@ -193,7 +194,7 @@ .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* .. _Cuccuru2013: http://orione.crs4.it/ -This tool uses `Prokka`_, which is licensed separately. Please cite Seemann T. Prokka: Prokaryotic Genome Annotation System (in preparation). +This tool uses `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted* .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml </help> |
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| diff -r fffa1ae330ae -r 5c0030f52b83 readme.rst --- a/readme.rst Mon Dec 09 04:58:14 2013 -0500 +++ b/readme.rst Wed Jan 08 04:29:37 2014 -0500 |
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| @@ -11,30 +11,31 @@ - Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; - Perl modules: Bio::SeqIO from BioPerl_ >= 1.6.900, `XML::Simple`_; -- tbl2asn_ >= 21.0 is required. This dependency is not managed here since versions are increasing very rapidly; - SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper. .. _BioPerl: http://search.cpan.org/dist/BioPerl/ .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/ -.. _tbl2asn: http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/ Configuration ------------- -If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of threads allocated by the job runner according to the configuration of the job destination selected for this tool (see http://wiki.galaxyproject.org/Admin/Config/Jobs ). +prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). -If instead you are using an older Galaxy release, you should add a line +If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. + +If instead you are using an older Galaxy release, you should also add a line GALAXY_SLOTS=N; export GALAXY_SLOTS -(where N is the number of threads allocated by the job runner) to the file +(where N is the number of CPU cores allocated by the job runner for this tool) to the file <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh Version history --------------- +- Release 4 (prokka 1.3.0): Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 (requires Galaxy release_2013.11.04 or later). Update citation. - Release 3 (prokka 1.2.0): 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). - Release 2 (prokka 1.1.0): Merge the wrappers by CRS4 and Lionel Guy. Directly call prokka, remove prokka.py . Add 'locustag', 'increment', 'gffver', 'compliant', 'addgenes', 'genus', 'species', 'strain', 'plasmid', 'gcode', 'usegenus', 'metagenome', 'fast', 'evalue', 'norrna', 'notrna' params. Upgrade BLAST+ dependency to v. 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst . - Release 1 (prokka 1.0.1): Add txt output file. Use a definition list instead of a block quote in <help>. Correct 2 dependency minimum versions. |
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| diff -r fffa1ae330ae -r 5c0030f52b83 tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 09 04:58:14 2013 -0500 +++ b/tool_dependencies.xml Wed Jan 08 04:29:37 2014 -0500 |
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| @@ -12,6 +12,9 @@ <package name="prodigal" version="2.60"> <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> + <package name="tbl2asn" version="22.4"> + <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> <package name="gnu_parallel" version="20131122"> <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> @@ -21,10 +24,14 @@ <package name="infernal" version="1.1"> <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> - <package name="prokka" version="1.7"> + <package name="minced" version="0.1.4"> + <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="prokka" version="1.8"> <install version="1.0"> <actions> <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> + <action target_filename="prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> @@ -39,8 +46,7 @@ Dependencies of Prokka which needs to be installed separately: - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; -- Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) >= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ); -- tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) >= 21.0 . +- Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) >= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ). 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. </readme> |