Mercurial > repos > nilesh > sickle_dev

comparison tool_dependencies.xml @ 3:13837e38aad2

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depending on zlib dependency
author nilesh
date Mon, 15 Jul 2013 11:08:48 -0500
parents b04d24abd573
children 4ce18088b3f2
comparison
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2:b04d24abd573 3:13837e38aad2
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="zlib" version="1.2.8"> 3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="6d14a9059f07" name="zlib" owner="nilesh" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="sickle" version="1.21.0">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <actions>
6 <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action> 9 <action type="set_environment_for_install">
7 <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action> 10 <repository changeset_revision="6d14a9059f07" name="zlib" owner="nilesh" toolshed="http://testtoolshed.g2.bx.psu.edu">
8 <action type="shell_command">make</action> 11 <package name="zlib" version="1.2.8" />
9 <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action> 12 </repository>
10 <action type="set_environment">
11 <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable>
12 </action> 13 </action>
13 </actions>
14 </install>
15 <readme>
16 Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source. It also requires zlib, which is included in this repo.
17 </readme>
18 </package>
19 <package name="sickle" version="1.21.0">
20 <install version="1.0">
21 <actions>
22 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action> 14 <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action>
23 <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action> 15 <action type="shell_command">make LIBS="-L$ZLIB_PATH -lz"</action>
24 <action type="move_file"> 16 <action type="move_file">
25 <source>sickle</source> 17 <source>sickle</source>
26 <destination>$INSTALL_DIR/bin</destination> 18 <destination>$INSTALL_DIR/bin</destination>
27 </action> 19 </action>
28 <action type="set_environment"> 20 <action type="set_environment">