| Previous changeset 6:3ad7ef0ba385 (2014-10-27) Next changeset 8:392255fa7ab9 (2016-10-28) |
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Commit message:
Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. |
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modified:
COPYING prokka.xml readme.rst tool_dependencies.xml |
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| diff -r 3ad7ef0ba385 -r f5e44aad6498 COPYING --- a/COPYING Mon Oct 27 06:45:52 2014 -0400 +++ b/COPYING Thu Oct 01 14:14:06 2015 -0400 |
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| @@ -1,8 +1,9 @@ +Copyright © 2015 The Genome Analysis Centre http://www.tgac.ac.uk/ Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ Copyright © 2013 Lionel Guy Created by: Paolo Uva <paolo.uva@crs4.it> -Nicola Soranzo <nicola.soranzo@crs4.it> +Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Lionel Guy <lionel.guy@icm.uu.se> Philip Mabon <philipmabon@gmail.com> |
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| diff -r 3ad7ef0ba385 -r f5e44aad6498 prokka.xml --- a/prokka.xml Mon Oct 27 06:45:52 2014 -0400 +++ b/prokka.xml Thu Oct 01 14:14:06 2015 -0400 |
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| @@ -1,16 +1,16 @@ -<tool id="prokka" name="Prokka" version="1.4.0"> +<tool id="prokka" name="Prokka" version="1.11.0"> <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="2.2.31">blast+</requirement> + <requirement type="package" version="3.1b2">hmmer</requirement> <requirement type="package" version="1.2.36">aragorn</requirement> <requirement type="package" version="2.60">prodigal</requirement> - <requirement type="package" version="23.7">tbl2asn</requirement> + <requirement type="package" version="24.3">tbl2asn</requirement> <requirement type="package" version="20131122">gnu_parallel</requirement> - <requirement type="package" version="0.5">barrnap</requirement> + <requirement type="package" version="0.7">barrnap</requirement> <requirement type="package" version="1.1">infernal</requirement> <requirement type="package" version="0.1.6">minced</requirement> - <requirement type="package" version="1.10">prokka</requirement> + <requirement type="package" version="1.11">prokka</requirement> </requirements> <version_command>prokka --version</version_command> <command> @@ -200,16 +200,6 @@ You can use this tool only if you agree to the license terms of: `Prokka`_. .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml - -If you use this tool, please cite: - -- |Cuccuru2014|_ -- |Seemann2014|_. - -.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929 -.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 -.. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069 -.. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068 </help> <citations> <citation type="doi">10.1093/bioinformatics/btu135</citation> |
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| diff -r 3ad7ef0ba385 -r f5e44aad6498 readme.rst --- a/readme.rst Mon Oct 27 06:45:52 2014 -0400 +++ b/readme.rst Thu Oct 01 14:14:06 2015 -0400 |
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| @@ -24,17 +24,10 @@ 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 CPU cores allocated by the job runner for this tool) to the file - - <tool_dependencies_dir>/prokka/1.10/crs4/prokka/<hash_string>/env.sh - Version history --------------- +- Release 7 (prokka 1.11.0): Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. - Release 6 (prokka 1.4.0): 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>. - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation. - 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. |
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| diff -r 3ad7ef0ba385 -r f5e44aad6498 tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 27 06:45:52 2014 -0400 +++ b/tool_dependencies.xml Thu Oct 01 14:14:06 2015 -0400 |
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| @@ -1,25 +1,25 @@ <?xml version="1.0"?> <tool_dependency> - <package name="blast+" version="2.2.28"> - <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="blast+" version="2.2.31"> + <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="hmmer" version="3.1b1"> - <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="hmmer" version="3.1b2"> + <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="aragorn" version="1.2.36"> <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="prodigal" version="2.60"> - <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9ec3f1e9198e" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="tbl2asn" version="23.7"> - <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="tbl2asn" version="24.3"> + <repository changeset_revision="41764d6a6a3c" name="package_tbl2asn_24_3" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="gnu_parallel" version="20131122"> <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="barrnap" version="0.5"> - <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="barrnap" version="0.7"> + <repository changeset_revision="c46ab932a19b" name="package_barrnap_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="infernal" version="1.1"> <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -27,10 +27,10 @@ <package name="minced" version="0.1.6"> <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="prokka" version="1.10"> + <package name="prokka" version="1.11"> <install version="1.0"> <actions> - <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action> + <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.11.tar.gz</action> <action type="shell_command">bin/prokka --setupdb</action> <action type="move_directory_files"> <source_directory>.</source_directory> @@ -42,13 +42,11 @@ </actions> </install> <readme> -Warning: Prokka includes custom databases and is thus about a 340 MB download! +Warning: Prokka includes custom databases and is thus about a 360 MB download! 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/ ). - -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> </package> </tool_dependency> |