Mercurial > repos > yating-l > hubarchivecreator
diff tool_dependencies.xml @ 51:364b8db8de17 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
| author | yating-l |
|---|---|
| date | Wed, 12 Apr 2017 16:51:03 -0400 |
| parents | 3e0c61b52a06 |
| children | c66803bff0cc |
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--- a/tool_dependencies.xml Fri Dec 30 14:05:48 2016 -0500 +++ b/tool_dependencies.xml Wed Apr 12 16:51:03 2017 -0400 @@ -13,120 +13,26 @@ - samtools - pslToBigPsl --> - <package name="ucsc_tools" version="312"> - <repository changeset_revision="ceda74761368" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - - <!-- TODO: Tools to install --> - <!-- twoBitInfo / bedToBigBed / faToTwoBit --> - - - <!-- Package gff3ToGenePred --> - <package name="gff3ToGenePred" version="0.0.1"> + + <package name="ucsc_tools_340" version="1.0"> <install version="1.0"> - <actions> - <action target_directory="bin" type="download_binary"> - <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template> - <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template> - </action> - <action type="chmod"> - <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>The tools downloaded by this dependency definition are free for academic use.</readme> - </package> - - <!-- Package gtfToGenePred --> - <package name="gtfToGenePred" version="0.0.1"> - <install version="1.0"> - <actions> - <action target_directory="bin" type="download_binary"> - <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template> - <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template> - </action> - <action type="chmod"> - <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file> - </action> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> - </actions> - </install> - <readme>The tools downloaded by this dependency definition are free for academic use.</readme> - </package> - - <!-- Package genePredToBed --> - <package name="genePredToBed" version="0.0.1"> - <install version="1.0"> - <actions> - <action target_directory="bin" type="download_binary"> - <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template> - <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template> - </action> - <action type="chmod"> - <file mode="750">$INSTALL_DIR/bin/genePredToBed</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>The tools downloaded by this dependency definition are free for academic use.</readme> + </actions_group> + </install> + <readme>The well known UCSC tools from Jim Kent.</readme> </package> - - http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred - - <!-- Package genePredToBigGenePred --> - <package name="genePredToBigGenePred" version="0.0.1"> - <install version="1.0"> - <actions> - <action target_directory="bin" type="download_binary"> - <url_template os="darwin"> - http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred - </url_template> - <url_template os="linux"> - http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred - </url_template> - </action> - <action type="chmod"> - <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>The tools downloaded by this dependency definition are free for academic use.</readme> - </package> - - <!-- Package pslToBigPsl --> - <package name="pslToBigPsl" version="0.0.1"> - <install version="1.0"> - <actions> - <action target_directory="bin" type="download_binary"> - <url_template os="darwin"> - http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl - </url_template> - <url_template os="linux"> - http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl - </url_template> - </action> - <action type="chmod"> - <file mode="750">$INSTALL_DIR/bin/pslToBigPsl</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>The tools downloaded by this dependency definition are free for academic use.</readme> - </package> + </tool_dependency>