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comparison tool_dependencies.xml @ 0:f493979f1408 draft default tip

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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
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-1:000000000000 0:f493979f1408
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 - genePredToBigGenePred
12 - faToTwoBit
13 - samtools
14 - pslToBigPsl
15 -->
16 <package name="ucsc_tools" version="312">
17 <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
18 </package>
19
20 <package name="samtools" version="1.2">
21 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
22 </package>
23
24 <!-- TODO: Tools to install -->
25 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
26
27
28 <!-- Package gff3ToGenePred -->
29 <package name="gff3ToGenePred" version="0.0.1">
30 <install version="1.0">
31 <actions>
32 <action target_directory="bin" type="download_binary">
33 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template>
34 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template>
35 </action>
36 <action type="chmod">
37 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
38 </action>
39 <action type="set_environment">
40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
41 </action>
42 </actions>
43 </install>
44 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
45 </package>
46
47 <!-- Package gtfToGenePred -->
48 <package name="gtfToGenePred" version="0.0.1">
49 <install version="1.0">
50 <actions>
51 <action target_directory="bin" type="download_binary">
52 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
53 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
54 </action>
55 <action type="chmod">
56 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
57 </action>
58 <action type="set_environment">
59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
60 </action>
61 </actions>
62 </install>
63 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
64 </package>
65
66 <!-- Package genePredToBed -->
67 <package name="genePredToBed" version="0.0.1">
68 <install version="1.0">
69 <actions>
70 <action target_directory="bin" type="download_binary">
71 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
72 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
73 </action>
74 <action type="chmod">
75 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
76 </action>
77 <action type="set_environment">
78 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
79 </action>
80 </actions>
81 </install>
82 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
83 </package>
84
85 http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred
86
87 <!-- Package genePredToBigGenePred -->
88 <package name="genePredToBigGenePred" version="0.0.1">
89 <install version="1.0">
90 <actions>
91 <action target_directory="bin" type="download_binary">
92 <url_template os="darwin">
93 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred
94 </url_template>
95 <url_template os="linux">
96 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred
97 </url_template>
98 </action>
99 <action type="chmod">
100 <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file>
101 </action>
102 <action type="set_environment">
103 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
104 </action>
105 </actions>
106 </install>
107 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
108 </package>
109
110 <!-- Package pslToBigPsl -->
111 <package name="pslToBigPsl" version="0.0.1">
112 <install version="1.0">
113 <actions>
114 <action target_directory="bin" type="download_binary">
115 <url_template os="darwin">
116 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl
117 </url_template>
118 <url_template os="linux">
119 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl
120 </url_template>
121 </action>
122 <action type="chmod">
123 <file mode="750">$INSTALL_DIR/bin/pslToBigPsl</file>
124 </action>
125 <action type="set_environment">
126 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
127 </action>
128 </actions>
129 </install>
130 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
131 </package>
132 </tool_dependency>