Mercurial > repos > crs4 > sequel
changeset 2:208ce57f9221 draft default tip
Fix version for blat requirement (reported by Bjoern Gruening). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation.
| author | crs4 |
|---|---|
| date | Fri, 18 Jul 2014 09:19:43 -0400 |
| parents | ccadfae70b02 |
| children | |
| files | readme.rst sequel_wrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 16 insertions(+), 12 deletions(-) [+] |
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--- a/readme.rst Wed Mar 05 06:48:08 2014 -0500 +++ b/readme.rst Fri Jul 18 09:19:43 2014 -0400 @@ -19,6 +19,7 @@ Version history --------------- +- Release 2: Fix version for blat requirement (reported by Björn Grüning). Upgrade BWA dependency to v. 0.7.7 . Update Orione citation. - Release 1: Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation. - Release 0: Initial release in the Tool Shed.
--- a/sequel_wrapper.xml Wed Mar 05 06:48:08 2014 -0500 +++ b/sequel_wrapper.xml Fri Jul 18 09:19:43 2014 -0400 @@ -1,8 +1,8 @@ <tool id="sequel_wrapper" name="SEQuel" version="0.2"> <description></description> <requirements> - <requirement type="package" version="0.6.2">bwa</requirement> - <requirement type="package" version="35">blat</requirement> + <requirement type="package" version="0.7.7">bwa</requirement> + <requirement type="package" version="35x1">blat</requirement> <requirement type="package" version="1.0.2">sequel</requirement> </requirements> <command interpreter="python"> @@ -112,19 +112,22 @@ **License and citation** -This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: http://opensource.org/licenses/MIT -If you use this tool in Galaxy, please cite |Cuccuru2013|_. - -.. |Cuccuru2013| 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*, accepted -.. _Cuccuru2013: http://orione.crs4.it/ - -This tool uses `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_. +You can use this tool only if you agree to the license terms of: `SEQuel`_. .. _SEQuel: http://bix.ucsd.edu/SEQuel/ + +If you use this tool, please cite: + +- |Cuccuru2014|_ +- |Ronen2012|_. + +.. |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 .. |Ronen2012| replace:: Ronen R., *et al.* (2012) SEQuel: improving the accuracy of genome assemblies. *Bioinformatics* 28 (12), i188-i196 .. _Ronen2012: http://bioinformatics.oxfordjournals.org/content/28/12/i188 </help>
--- a/tool_dependencies.xml Wed Mar 05 06:48:08 2014 -0500 +++ b/tool_dependencies.xml Fri Jul 18 09:19:43 2014 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bwa" version="0.6.2"> - <repository changeset_revision="0778635a84ba" name="package_bwa_0_6_2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="bwa" version="0.7.7"> + <repository changeset_revision="def70e393020" name="package_bwa_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> - <package name="blat" version="35"> + <package name="blat" version="35x1"> <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="sequel" version="1.0.2">