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comparison tool_dependencies.xml @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
parents 1ea6445491d4
children 4fe2e80d4ae1
comparison
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10:f65857c1b92e 11:b22f8634ff84
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="defuse" version="0.6.0"> 3 <package name="defuse" version="0.6.2">
4 <install version="1.0"> 4 <repository changeset_revision="5a4237bbe6bf" name="package_defuse_0_6_2" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
5 <actions>
6 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
7 <action type="shell_command">cd tools &amp;&amp; make</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 <action type="set_environment">
13 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
14 </action>
15 </actions>
16 </install>
17 <readme>
18 deFuse code
19 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
20 </readme>
21 </package> 5 </package>
22 6 <package name="samtools" version="0.1.19">
23 <package name="samtools" version="0.1.18"> 7 <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
24 <install version="1.0">
25 <actions>
26 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
27 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
28 <action type="shell_command">make</action>
29 <action type="move_file">
30 <source>samtools</source>
31 <destination>$INSTALL_DIR/bin</destination>
32 </action>
33 <action type="move_file">
34 <source>misc/maq2sam-long</source>
35 <destination>$INSTALL_DIR/bin</destination>
36 </action>
37 <action type="set_environment">
38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
39 </action>
40 </actions>
41 </install>
42 <readme>
43 Compiling SAMtools requires the ncurses and zlib development libraries.
44 </readme>
45 </package> 8 </package>
46 9 <package name="bowtie" version="1.0.0">
47 10 <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
48 <package name="bowtie" version="0.12.7">
49 <install version="1.0">
50 <actions>
51 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
52 <action type="shell_command">make</action>
53 <action type="move_file">
54 <source>bowtie</source>
55 <destination>$INSTALL_DIR/bin</destination>
56 </action>
57 <action type="move_file">
58 <source>bowtie-build</source>
59 <destination>$INSTALL_DIR/bin</destination>
60 </action>
61 <action type="move_file">
62 <source>bowtie-inspect</source>
63 <destination>$INSTALL_DIR/bin</destination>
64 </action>
65 <action type="set_environment">
66 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
67 </action>
68 </actions>
69 </install>
70 <readme>
71 Compiling Bowtie requires libpthread to be present on your system.
72 </readme>
73 </package> 11 </package>
74 12 <package name="gmap" version="2013-05-09">
75 <package name="gmap" version="2012-07-20"> 13 <repository changeset_revision="953f5eb53593" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
76 <install version="1.0">
77 <actions>
78 <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action>
79 <action type="shell_command">./configure</action>
80 <action type="shell_command">make</action>
81 <action type="move_file">
82 <source>src/gmap</source>
83 <destination>$INSTALL_DIR/bin</destination>
84 </action>
85 <action type="move_file">
86 <source>src/gmapindex</source>
87 <destination>$INSTALL_DIR/bin</destination>
88 </action>
89 <action type="move_file">
90 <source>src/gsnap</source>
91 <destination>$INSTALL_DIR/bin</destination>
92 </action>
93 <action type="move_file">
94 <source>src/uniqscan</source>
95 <destination>$INSTALL_DIR/bin</destination>
96 </action>
97 <action type="move_file">
98 <source>src/iit_store</source>
99 <destination>$INSTALL_DIR/bin</destination>
100 </action>
101 <action type="move_file">
102 <source>src/iit_get</source>
103 <destination>$INSTALL_DIR/bin</destination>
104 </action>
105 <action type="move_file">
106 <source>src/atoiindex</source>
107 <destination>$INSTALL_DIR/bin</destination>
108 </action>
109 <action type="move_file">
110 <source>src/snpindex</source>
111 <destination>$INSTALL_DIR/bin</destination>
112 </action>
113 <action type="move_file">
114 <source>src/cmetindex</source>
115 <destination>$INSTALL_DIR/bin</destination>
116 </action>
117 <action type="move_file">
118 <source>src/get-genome</source>
119 <destination>$INSTALL_DIR/bin</destination>
120 </action>
121 <action type="move_directory_files">
122 <source_directory>util</source_directory>
123 <destination_directory>$INSTALL_DIR/bin</destination_directory>
124 </action>
125 <action type="set_environment">
126 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
127 </action>
128 </actions>
129 </install>
130 <readme>
131 </readme>
132 </package> 14 </package>
133 15 <package name="blat" version="35x1">
134 <package name="blat" version="34x10"> 16 <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
135 <install version="1.0">
136 <actions>
137 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
138 <action type="shell_command">chmod 755 blat</action>
139 <action type="move_file">
140 <source>blat</source>
141 <destination>$INSTALL_DIR/bin</destination>
142 </action>
143 <action type="set_environment">
144 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
145 </action>
146 </actions>
147 </install>
148 <readme>
149 This only handles blat for a non-commercial linux system.
150
151 Please note that the Blat source and executables are freely available for
152 academic, nonprofit and personal use. Commercial licensing information is
153 available on the Kent Informatics website (http://www.kentinformatics.com/).
154 </readme>
155 </package> 17 </package>
156 18 <package name="R" version="3.1.2">
157 <package name="fatotwobit" version="34x10"> 19 <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
158 <install version="1.0">
159 <actions>
160 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
161 <action type="shell_command">chmod 755 faToTwoBit</action>
162 <action type="move_file">
163 <source>faToTwoBit</source>
164 <destination>$INSTALL_DIR/bin</destination>
165 </action>
166 <action type="set_environment">
167 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
168 </action>
169 </actions>
170 </install>
171 <readme>
172 This only handles faToTwoBit for a non-commercial linux system.
173
174 Please note that the source and executables are freely available for
175 academic, nonprofit and personal use. Commercial licensing information is
176 available on the Kent Informatics website (http://www.kentinformatics.com/).
177 </readme>
178 </package> 20 </package>
179 21 <package name="ada" version="2.0.3">
22 <repository changeset_revision="f0e6af8a95e5" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />
23 </package>
180 </tool_dependency> 24 </tool_dependency>