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tool_dependencies.xml
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tool_dependencies.xml
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<?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 name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True"/>
</package>
<package name="samtools" version="1.2">
<repository name="package_samtools_1_2" owner="iuc" prior_installation_required="True"/>
</package>
<!-- TODO: Tools to install -->
<!-- twoBitInfo / bedToBigBed / faToTwoBit -->
<!-- Package gff3ToGenePred -->
<package name="gff3ToGenePred" version="0.0.1">
<install version="1.0">
<actions>
<action type="download_binary" target_directory="bin">
<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">$INSTALL_DIR/bin/gff3ToGenePred</file>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$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 type="download_binary" target_directory="bin">
<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">$INSTALL_DIR/bin/gtfToGenePred</file>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$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 type="download_binary" target_directory="bin">
<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">$INSTALL_DIR/bin/genePredToBed</file>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$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 type="download_binary" target_directory="bin">
<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">$INSTALL_DIR/bin/genePredToBigGenePred</file>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$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 type="download_binary" target_directory="bin">
<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">$INSTALL_DIR/bin/pslToBigPsl</file>
</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$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>