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comparison tool_dependencies.xml @ 25:09e6427d3e6a draft

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Use repository dependency for samtools
author Jim Johnson <jj@umn.edu>
date Mon, 18 Feb 2013 11:01:18 -0600
parents 7533db8dfb5b
children bac82f25d42a
comparison
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24:6460f2ba6a60 25:09e6427d3e6a
43 for the local installation. 43 for the local installation.
44 44
45 </readme> 45 </readme>
46 </package> 46 </package>
47 <package name="samtools" version="0.1.18"> 47 <package name="samtools" version="0.1.18">
48 <install version="1.0"> 48 <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_samtools_0_1_18" owner="devteam" changeset_revision="a7936f4ea405" />
49 <actions>
50 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
51 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
52 <action type="shell_command">make</action>
53 <action type="move_file">
54 <source>samtools</source>
55 <destination>$INSTALL_DIR/bin</destination>
56 </action>
57 <action type="move_file">
58 <source>misc/maq2sam-long</source>
59 <destination>$INSTALL_DIR/bin</destination>
60 </action>
61 <action type="set_environment">
62 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
63 </action>
64 </actions>
65 </install>
66 <readme>
67 Compiling SAMtools requires the ncurses and zlib development libraries.
68 </readme>
69 </package> 49 </package>
70 </tool_dependency> 50 </tool_dependency>