Mercurial > repos > biomonika > test_dependency
changeset 9:480491c2ce1c
freebayes_inspired
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Mon, 25 Aug 2014 13:29:42 -0400 |
| parents | 5573c2fa9824 |
| children | 66d7b41f74b1 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 20 insertions(+), 5 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Aug 25 12:51:30 2014 -0400 +++ b/tool_dependencies.xml Mon Aug 25 13:29:42 2014 -0400 @@ -2,13 +2,28 @@ <set_environment version="1.0"> <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - <package name="samtools_fPIC" version="1.1"> + + <package name="samtools" version="0.1.18"> <install version="1.0"> <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> - <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile </action> - <action type="shell_command">make </action> - <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> + <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>libbam.a</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bam.h</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> <action type="set_environment"> <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</environment_variable> </action>