Mercurial > repos > rmarenco > hubarchivecreator

comparison tool_dependencies.xml @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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children df9e12da0d13
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0:0f3bc17e5ede 1:fb5e60d4d18a
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <!-- UCSC Tools in -->
4 <!-- Useful for HAC are:
5 - twoBitInfo
6 - sort
7 - bedToBigBed
8 - gff3ToGenePred
9 - gtfToGenePred
10 - genePredToBed
11 - faToTwoBit
12 - samtools
13 -->
14 <package name="ucsc_tools" version="312">
15 <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
16 </package>
17
18 <package name="samtools" version="1.2">
19 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
20 </package>
21
22 <!-- TODO: Tools to install -->
23 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
24
25
26 <!-- Package gff3ToGenePred -->
27 <package name="gff3ToGenePred" version="0.0.1">
28 <install version="1.0">
29 <actions>
30 <action target_directory="bin" type="download_binary">
31 <url_template os="darwin">
32 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred
33 </url_template>
34 <url_template os="linux">
35 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred
36 </url_template>
37 </action>
38 <action type="chmod">
39 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
40 </action>
41 <action type="set_environment">
42 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
43 </action>
44 </actions>
45 </install>
46 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
47 </package>
48
49 <!-- Package gtfToGenePred -->
50 <package name="gtfToGenePred" version="0.0.1">
51 <install version="1.0">
52 <actions>
53 <action target_directory="bin" type="download_binary">
54 <url_template os="darwin">
55 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred
56 </url_template>
57 <url_template os="linux">
58 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred
59 </url_template>
60 </action>
61 <action type="chmod">
62 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
63 </action>
64 <action type="set_environment">
65 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
66 </action>
67 </actions>
68 </install>
69 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
70 </package>
71
72 <!-- Package genePredToBed -->
73 <package name="genePredToBed" version="0.0.1">
74 <install version="1.0">
75 <actions>
76 <action target_directory="bin" type="download_binary">
77 <url_template os="darwin">
78 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed
79 </url_template>
80 <url_template os="linux">
81 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed
82 </url_template>
83 </action>
84 <action type="chmod">
85 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
86 </action>
87 <action type="set_environment">
88 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
89 </action>
90 </actions>
91 </install>
92 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
93 </package>
94 </tool_dependency>