Mercurial > repos > rmarenco > hubarchivecreator

comparison tool_dependencies.xml @ 20:40469b265ddb draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
author yating-l
date Fri, 20 Jan 2017 17:12:03 -0500
parents d786bca6a75d
children fcc1021bd496
comparison
equal deleted inserted replaced
19:0152500d9acd 20:40469b265ddb
9 - gtfToGenePred 9 - gtfToGenePred
10 - genePredToBed 10 - genePredToBed
11 - genePredToBigGenePred 11 - genePredToBigGenePred
12 - faToTwoBit 12 - faToTwoBit
13 - samtools 13 - samtools
14 - pslToBigPsl
14 --> 15 -->
15 <package name="ucsc_tools" version="312">
16 <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package>
18
19 <package name="samtools" version="1.2"> 16 <package name="samtools" version="1.2">
20 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 17 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
21 </package> 18 </package>
22 19
23 <!-- TODO: Tools to install --> 20 <package name="ucsc_tools_340" version="1.0">
24 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
25
26
27 <!-- Package gff3ToGenePred -->
28 <package name="gff3ToGenePred" version="0.0.1">
29 <install version="1.0"> 21 <install version="1.0">
30 <actions> 22 <actions_group>
31 <action target_directory="bin" type="download_binary"> 23 <actions architecture="x86_64" os="linux">
32 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template> 24 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
33 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template> 25 <action type="move_directory_files">
34 </action> 26 <source_directory>.</source_directory>
35 <action type="chmod"> 27 <destination_directory>$INSTALL_DIR/bin</destination_directory>
36 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file> 28 </action>
37 </action> 29 </actions>
38 <action type="set_environment"> 30 <action type="set_environment">
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
40 </action> 32 </action>
41 </actions> 33 </actions_group>
42 </install> 34 </install>
43 <readme>The tools downloaded by this dependency definition are free for academic use.</readme> 35 <readme>The well known UCSC tools from Jim Kent.</readme>
44 </package> 36 </package>
45 37
46 <!-- Package gtfToGenePred -->
47 <package name="gtfToGenePred" version="0.0.1">
48 <install version="1.0">
49 <actions>
50 <action target_directory="bin" type="download_binary">
51 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
52 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
53 </action>
54 <action type="chmod">
55 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
56 </action>
57 <action type="set_environment">
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
59 </action>
60 </actions>
61 </install>
62 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
63 </package>
64
65 <!-- Package genePredToBed -->
66 <package name="genePredToBed" version="0.0.1">
67 <install version="1.0">
68 <actions>
69 <action target_directory="bin" type="download_binary">
70 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
71 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
72 </action>
73 <action type="chmod">
74 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
75 </action>
76 <action type="set_environment">
77 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
78 </action>
79 </actions>
80 </install>
81 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
82 </package>
83
84 http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred
85
86 <!-- Package genePredToBigGenePred -->
87 <package name="genePredToBigGenePred" version="0.0.1">
88 <install version="1.0">
89 <actions>
90 <action target_directory="bin" type="download_binary">
91 <url_template os="darwin">
92 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred
93 </url_template>
94 <url_template os="linux">
95 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred
96 </url_template>
97 </action>
98 <action type="chmod">
99 <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file>
100 </action>
101 <action type="set_environment">
102 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
103 </action>
104 </actions>
105 </install>
106 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
107 </package>
108 </tool_dependency> 38 </tool_dependency>