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comparison tool_dependencies.xml @ 5:3bd1087db05e draft

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Add dependecies for bowtie, blat, and faToTwoBit
author Jim Johnson <jj@umn.edu>
date Fri, 04 Jan 2013 15:01:19 -0600
parents 679a5c7b1294
children 1ea6445491d4
comparison
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4:679a5c7b1294 5:3bd1087db05e
16 </install> 16 </install>
17 <readme> 17 <readme>
18 </readme> 18 </readme>
19 </package> 19 </package>
20 20
21 <package name="bowtie" version="0.12.7">
22 <install version="1.0">
23 <actions>
24 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
25 <action type="shell_command">make</action>
26 <action type="move_file">
27 <source>bowtie</source>
28 <destination>$INSTALL_DIR/bin</destination>
29 </action>
30 <action type="move_file">
31 <source>bowtie-build</source>
32 <destination>$INSTALL_DIR/bin</destination>
33 </action>
34 <action type="move_file">
35 <source>bowtie-inspect</source>
36 <destination>$INSTALL_DIR/bin</destination>
37 </action>
38 <action type="set_environment">
39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
40 </action>
41 </actions>
42 </install>
43 <readme>
44 Compiling Bowtie requires libpthread to be present on your system.
45 </readme>
46 </package>
47
48 <package name="blat" version="34x10">
49 <install version="1.0">
50 <actions>
51 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
52 <action type="shell_command">chmod 755 blat</action>
53 <action type="move_file">
54 <source>blat</source>
55 <destination>$INSTALL_DIR/bin</destination>
56 </action>
57 <action type="set_environment">
58 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
59 </action>
60 </actions>
61 </install>
62 <readme>
63 This only handles blat for a non-commercial linux system.
64
65 Please note that the Blat source and executables are freely available for
66 academic, nonprofit and personal use. Commercial licensing information is
67 available on the Kent Informatics website (http://www.kentinformatics.com/).
68 </readme>
69 </package>
70
71 <package name="fatotwobit" version="34x10">
72 <install version="1.0">
73 <actions>
74 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
75 <action type="shell_command">chmod 755 faToTwoBit</action>
76 <action type="move_file">
77 <source>faToTwoBit</source>
78 <destination>$INSTALL_DIR/bin</destination>
79 </action>
80 <action type="set_environment">
81 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
82 </action>
83 </actions>
84 </install>
85 <readme>
86 This only handles faToTwoBit for a non-commercial linux system.
87
88 Please note that the source and executables are freely available for
89 academic, nonprofit and personal use. Commercial licensing information is
90 available on the Kent Informatics website (http://www.kentinformatics.com/).
91 </readme>
92 </package>
93
21 </tool_dependency> 94 </tool_dependency>