| Previous changeset 1:ab12adaa5cc2 (2013-07-06) |
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readme.rst tool_dependencies.xml |
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| diff -r ab12adaa5cc2 -r b1ad88bbc5fa readme.rst --- a/readme.rst Sat Jul 06 10:34:27 2013 -0400 +++ b/readme.rst Mon Aug 12 11:55:07 2013 -0400 |
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| @@ -6,18 +6,18 @@ This is a wrapper for the command line tool of Glimmer3_. -.. _Glimmer: http://www.cbcb.umd.edu/software/glimmer/ +.. _Glimmer3: http://www.cbcb.umd.edu/software/glimmer/ Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. -S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548. +| S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548. -A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641. +| A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641. -A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). +| A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). ============ |
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| diff -r ab12adaa5cc2 -r b1ad88bbc5fa tool_dependencies.xml --- a/tool_dependencies.xml Sat Jul 06 10:34:27 2013 -0400 +++ b/tool_dependencies.xml Mon Aug 12 11:55:07 2013 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.61"> - <repository changeset_revision="5d0c54f7fea2" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b482933a6de5" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <set_environment version="1.0"> <environment_variable action="set_to" name="GLIMMER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> |