annotate tool_dependencies.xml @ 14:cdb7231da7f2 draft

Uploaded
author fcaramia
date Mon, 17 Jun 2013 21:44:43 -0400
parents
children d2ba233899b0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
1 <?xml version="1.0"?>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
2 <tool_dependency>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
3 <set_environment version="1.0">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
5 </set_environment>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
6 <package name="bowtie2" version="2.0.0-beta7">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
7 <install version="1.0">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
8 <actions>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
9 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
10 <action type="shell_command">make</action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
11 <action type="move_file">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
12 <source>bowtie2</source>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
13 <destination>$INSTALL_DIR/bin</destination>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
14 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
15 <action type="move_file">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
16 <source>bowtie2-align</source>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
17 <destination>$INSTALL_DIR/bin</destination>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
18 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
19 <action type="move_file">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
20 <source>bowtie2-build</source>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
21 <destination>$INSTALL_DIR/bin</destination>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
22 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
23 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
24 <action type="set_environment">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
26 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
27 </actions>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
28 </install>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
29 <readme>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
30 Compiling bowtie2 requires zlib and libpthread to be present on your system.
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
31 </readme>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
32 </package>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
33 <package name="bowtie" version="0.12.8">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
34 <install version="1.0">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
35 <actions>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
36 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
37 <action type="shell_command">make</action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
38 <action type="move_file">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
39 <source>bowtie</source>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
40 <destination>$INSTALL_DIR/bin</destination>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
41 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
42 <action type="move_file">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
43 <source>bowtie-inspect</source>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
44 <destination>$INSTALL_DIR/bin</destination>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
45 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
46 <action type="move_file">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
47 <source>bowtie-build</source>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
48 <destination>$INSTALL_DIR/bin</destination>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
49 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
50 <action type="set_environment">
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
52 </action>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
53 </actions>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
54 </install>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
55 <readme>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
56 </readme>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
57 </package>
cdb7231da7f2 Uploaded
fcaramia
parents:
diff changeset
58 </tool_dependency>