Mercurial > repos > lionelguy > prokka
changeset 8:6acf850bca99 draft
Replaced the repository_dependencies by tool_dependencies
| author | lionelguy |
|---|---|
| date | Fri, 06 Sep 2013 02:42:23 -0400 |
| parents | 39bc9c61c55b |
| children | 37e2aeda27f4 |
| files | repository_dependencies.xml tool_dependencies.xml |
| diffstat | 2 files changed, 41 insertions(+), 33 deletions(-) [+] |
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--- a/repository_dependencies.xml Thu Sep 05 07:42:05 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Prokka requires a suite of other tools"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="trna_prediction" owner="bgruening" changeset_revision="d34f31cbc9dd" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="barrnap" owner="simon-gladman" changeset_revision="a41418a3bd38" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="prodigal" owner="edward-kirton" changeset_revision="304c1a67bb7b" /> - <!--<repository toolshed="http://toolshed.g2.bx.psu.edu" name="infernal" owner="" changeset_revision="" /> --> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_hmmer_3_1" owner="lionelguy" changeset_revision="007c736bf7e8" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="ncbi_blast_plus" owner="devteam" changeset_revision="9dabbfd73c8a" /> -</repositories> \ No newline at end of file
--- a/tool_dependencies.xml Thu Sep 05 07:42:05 2013 -0400 +++ b/tool_dependencies.xml Fri Sep 06 02:42:23 2013 -0400 @@ -1,36 +1,53 @@ <?xml version="1.0"?> <tool_dependency> - <package name="prokka" version="1.7"> - <install version="1.0"> - <actions> + <package name="hmmer" version="3.1b1"> + <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="blast+" version="2.2.26+"> + <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="aragorn" version="1.2.36"> + <repository changeset_revision="d34f31cbc9dd" name="trna_prediction" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="prodigal" version="2.60"> + <repository changeset_revision="304c1a67bb7b" name="prodigal" owner="edward-kirton" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="package_barrnap_0_1" version="0.1"> + <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <!--<package name="infernal" version="1.1rc4"> + <repository name="package_infernal_1_1rc4" owner="iuc" /> + </package> --> + <package name="prokka" version="1.7"> + <install version="1.0"> + <actions> <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> <!-- Copying the whole bin, binaries, doc and db folders --> - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="make_directory">$INSTALL_DIR/binaries</action> - <action type="make_directory">$INSTALL_DIR/db</action> - <action type="make_directory">$INSTALL_DIR/doc</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/binaries</action> + <action type="make_directory">$INSTALL_DIR/db</action> + <action type="make_directory">$INSTALL_DIR/doc</action> <action type="move_directory_files"> - <source_directory>binaries</source_directory> - <destination_directory>$INSTALL_DIR/binaries</destination_directory> - </action> - <action type="move_directory_files"> - <source_directory>db</source_directory> - <destination_directory>$INSTALL_DIR/db</destination_directory> - </action> - <action type="move_directory_files"> - <source_directory>doc</source_directory> - <destination_directory>$INSTALL_DIR/doc</destination_directory> - </action> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="move_directory_files"> + <source_directory>binaries</source_directory> + <destination_directory>$INSTALL_DIR/binaries</destination_directory> + </action> + <action type="move_directory_files"> + <source_directory>db</source_directory> + <destination_directory>$INSTALL_DIR/db</destination_directory> + </action> + <action type="move_directory_files"> + <source_directory>doc</source_directory> + <destination_directory>$INSTALL_DIR/doc</destination_directory> + </action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> - <readme> This installs prokka 1.7 Note: this is about a 2.0 GB download due to included custom databases.</readme>