Mercurial > repos > yating-l > hubarchivecreator
diff tool_dependencies.xml @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
|---|---|
| date | Wed, 21 Dec 2016 12:13:04 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Dec 21 12:13:04 2016 -0500 @@ -0,0 +1,132 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- UCSC Tools in --> + <!-- Useful for HAC are: + - twoBitInfo + - sort + - bedToBigBed + - gff3ToGenePred + - gtfToGenePred + - genePredToBed + - genePredToBigGenePred + - faToTwoBit + - samtools + - pslToBigPsl + --> + <package name="ucsc_tools" version="312"> + <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <!-- TODO: Tools to install --> + <!-- twoBitInfo / bedToBigBed / faToTwoBit --> + + + <!-- Package gff3ToGenePred --> + <package name="gff3ToGenePred" 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.${architecture}/gff3ToGenePred</url_template> + <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${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">$INSTALL_DIR/bin/gtfToGenePred</file> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$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> + </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>