Mercurial > repos > iuc > package_blat_35x1
changeset 4:cc0f4b49b6f1 draft default tip
Uploaded
| author | iuc |
|---|---|
| date | Tue, 18 Feb 2014 12:52:26 -0500 |
| parents | b355179ea459 |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 18 insertions(+), 26 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Wed Jan 29 16:13:18 2014 -0500 +++ b/tool_dependencies.xml Tue Feb 18 12:52:26 2014 -0500 @@ -1,36 +1,28 @@ +<?xml version="1.0"?> <tool_dependency> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> <package name="blat" version="35x1"> <install version="1.0"> <actions> - - <action type="download_binary"> - <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</url_template> - <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template> - <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template> - <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat/blat</url_template> - </action> - - <action type="move_file"> - <source>$INSTALL_DIR/blat</source> - <destination>$INSTALL_DIR/blat</destination> - </action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/blat</file> + <!-- finally go back to the original version and compile blat and the entire server from source + Thanks to Nicola Soranzo. + The problem is that the binaries are not versioned and we can't guarantee reproducibility. + The only way to download the source code of minor releases is from the git repository. + --> + <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git blat</action> + <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action> + <action type="set_environment_for_install"> + <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> </action> + <action type="shell_command">export HOME=$INSTALL_DIR && export MACHTYPE=`uname -m` && export PNGINCL=-I${LIBPNG_ROOT}/include && export PNGLIB="-L${LIBPNG_ROOT}/lib -lpng" && mkdir -p $HOME/bin/$MACHTYPE && make -C src/lib/ && make -C src/jkOwnLib/ && make -C src/blat/ && mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ && rm -rf $INSTALL_DIR/.ccache/</action> <action type="set_environment"> - <environment_variable name="PATH" action="append_to">$INSTALL_DIR</environment_variable> - <environment_variable name="BLAT_PATH" action="append_to">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable> + <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable> </action> - - <!-- - Alternative version from Nicola Soranzo. - <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action> - <action type="shell_command">export MACHTYPE=`uname -m` && export HOME=$INSTALL_DIR && mkdir -p $HOME/bin/$MACHTYPE && make</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/`uname -m`</environment_variable> - </action> - --> - </actions> </install> <readme>