Mercurial > repos > nilesh > sickle_dev
changeset 10:341d297d8a85 default tip
Merge heads at 5:8a00afae9eca and 9:30f36c4faa39 which were created as a result of a recently fixed bug.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Mon, 13 Jan 2014 12:42:57 -0500 |
| parents | 30f36c4faa39 (diff) 8a00afae9eca (current diff) |
| children | |
| files | tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 11 deletions(-) [+] |
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--- a/sickle.xml Mon Jul 15 12:17:15 2013 -0400 +++ b/sickle.xml Mon Jan 13 12:42:57 2014 -0500 @@ -1,7 +1,6 @@ <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 12:17:15 2013 -0400 +++ b/tool_dependencies.xml Mon Jan 13 12:42:57 2014 -0500 @@ -1,20 +1,16 @@ <?xml version="1.0"?> <tool_dependency> - <package name="zlib" version="1.2.8"> - <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> <package name="sickle" version="1.21.0"> <install version="1.0"> <actions> - <action type="set_environment_for_install"> - <repository changeset_revision="28f618926504" name="zlib" owner="nilesh" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="zlib" version="1.2.8" /> - </repository> - </action> + <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action> + <action type="shell_command">make</action> + <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action> <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action> - <action type="shell_command">sickle make LIBS="-L$ZLIB_PATH -lz"</action> + <action type="shell_command">cd ./sickle && make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action> <action type="move_file"> - <source>sickle</source> + <source>sickle/sickle</source> <destination>.</destination> </action> <action type="set_environment">