Mercurial > repos > iuc > package_ucsc_tools_0_1

comparison tool_dependencies.xml @ 1:359b0988e735 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_ucsc_tools_0_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:19:23 -0400
parents 4e9561e890fe
children
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0:4e9561e890fe 1:359b0988e735
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool_dependency> 2 <tool_dependency>
3 <!-- This package will not track any version of the underlying toools.
4 Any hint how to compile or ship the binaries without violating the license is very much appreciated.
5 -->
6 <package name="ucsc_tools" version="0.1"> 3 <package name="ucsc_tools" version="0.1">
7 <install version="1.0"> 4 <install version="1.0">
8 <actions> 5 <actions_group>
9 <action type="download_binary"> 6 <actions architecture="x86_64" os="linux">
10 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> 7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/ucsc/ucsc-312-Linux-x86_64.tar.gz</action>
11 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> 8 <action type="shell_command">rm ucsc-312-Linux-x86_64.tar.gz</action>
12 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> 9 <action type="move_directory_files">
13 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template> 10 <source_directory>.</source_directory>
14 </action> 11 <destination_directory>$INSTALL_DIR</destination_directory>
15 <action type="chmod"> 12 </action>
16 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file> 13 </actions>
17 </action> 14 <!--actions architecture="x86_64" os="darwin">
18 <action type="download_binary"> 15 <action type="download_by_url"></action>
19 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template> 16 <action type="move_directory_files">
20 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template> 17 <source_directory>.</source_directory>
21 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template> 18 <destination_directory>$INSTALL_DIR/bin</destination_directory>
22 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template> 19 </action>
23 </action> 20 </actions-->
24 <action type="chmod">
25 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
26 </action>
27 <action type="download_binary">
28 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
29 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
30 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
31 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
32 </action>
33 <action type="chmod">
34 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
35 </action>
36 <action type="set_environment"> 21 <action type="set_environment">
37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> 22 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
23 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
38 <environment_variable name="UCSC_TOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> 24 <environment_variable name="UCSC_TOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
39 </action> 25 </action>
40 </actions> 26 </actions_group>
41 </install> 27 </install>
42 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> 28 <readme>The well known UCSC tools from Jim Kent.</readme>
43 </package> 29 </package>
44 </tool_dependency> 30 </tool_dependency>