Mercurial > repos > bgruening > bismark

comparison tool_dependencies.xml @ 0:62c6da72dd4a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Sat, 06 Jul 2013 09:57:36 -0400
parents
children 9d02cd7883ad
comparison
equal deleted inserted replaced
-1:000000000000 0:62c6da72dd4a
1 <?xml version="1.0"?>
2 <package name="samtools" version="0.1.18">
3 <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_samtools_0_1_18" owner="devteam " changeset_revision="a7936f4ea405" />
4 </package>
5 <tool_dependency>
6 <set_environment version="1.0">
7 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
8 </set_environment>
9 <package name="bowtie2" version="2.1.0">
10 <install version="1.0">
11 <actions>
12 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
13 <action type="shell_command">make</action>
14 <action type="move_file">
15 <source>bowtie2</source>
16 <destination>$INSTALL_DIR/bin</destination>
17 </action>
18 <action type="move_file">
19 <source>bowtie2-align</source>
20 <destination>$INSTALL_DIR/bin</destination>
21 </action>
22 <action type="move_file">
23 <source>bowtie2-build</source>
24 <destination>$INSTALL_DIR/bin</destination>
25 </action>
26 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
27 <action type="set_environment">
28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
29 </action>
30 </actions>
31 </install>
32 <readme>
33 Compiling bowtie2 requires zlib and libpthread to be present on your system.
34 </readme>
35 </package>
36 <package name="bowtie" version="0.12.8">
37 <install version="1.0">
38 <actions>
39 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
40 <action type="shell_command">make</action>
41 <action type="move_file">
42 <source>bowtie</source>
43 <destination>$INSTALL_DIR/bin</destination>
44 </action>
45 <action type="move_file">
46 <source>bowtie-inspect</source>
47 <destination>$INSTALL_DIR/bin</destination>
48 </action>
49 <action type="move_file">
50 <source>bowtie-build</source>
51 <destination>$INSTALL_DIR/bin</destination>
52 </action>
53 <action type="set_environment">
54 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
55 </action>
56 </actions>
57 </install>
58 <readme>
59 </readme>
60 </package>
61 </tool_dependency>
62
63
64