Mercurial > repos > nilesh > sickle_dev
changeset 2:b04d24abd573
separated into two dependencies
| author | nilesh |
|---|---|
| date | Mon, 15 Jul 2013 10:47:42 -0500 |
| parents | db0c767dbe09 |
| children | 13837e38aad2 |
| files | sickle.xml tool_dependencies.xml |
| diffstat | 2 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- a/sickle.xml Mon Jul 15 10:11:13 2013 -0500 +++ b/sickle.xml Mon Jul 15 10:47:42 2013 -0500 @@ -1,6 +1,7 @@ <tool id="sickle" name="Sickle"> <description>Windowed Adaptive Trimming of FastQ data</description> <requirements> + <requirement type="package" version="1.2.8">zlib</requirement> <requirement type="package" version="1.21.0">sickle</requirement> </requirements> <command>
--- a/tool_dependencies.xml Mon Jul 15 10:11:13 2013 -0500 +++ b/tool_dependencies.xml Mon Jul 15 10:47:42 2013 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sickle" version="1.21.0"> + <package name="zlib" version="1.2.8"> <install version="1.0"> <actions> <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action> @@ -10,8 +10,17 @@ <action type="set_environment"> <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable> </action> + </actions> + </install> + <readme> + Sickle requires a C compiler; GCC or clang are recommended. Sickle relies on Heng Li's kseq.h, which is bundled with the source. It also requires zlib, which is included in this repo. + </readme> + </package> + <package name="sickle" version="1.21.0"> + <install version="1.0"> + <actions> <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action> - <action type="shell_command">make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action> + <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action> <action type="move_file"> <source>sickle</source> <destination>$INSTALL_DIR/bin</destination>