Mercurial > repos > bgruening > upload_testing
changeset 53:a281b5931ffb
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 09 Aug 2013 14:04:34 -0400 |
| parents | 411c871f4cfd |
| children | 675d25a0b9d4 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 18 insertions(+), 57 deletions(-) [+] |
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--- a/tool_dependencies.xml Sat Aug 03 09:48:44 2013 -0400 +++ b/tool_dependencies.xml Fri Aug 09 14:04:34 2013 -0400 @@ -1,67 +1,28 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <package name="boost" version="1.53.0"> + <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="matplotlib" version="1.2.1"> - <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="scipy" version="0.12.0"> - <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - - - <package name="ucsc_tools" version="0.1"> + <package name="blast+" version="2.2.26+"> <install version="1.0"> <actions> - <action type="download_binary"> - <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> - <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> - <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template> - <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template> - </action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file> - </action> - <action type="download_binary"> - <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template> - <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template> - <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template> - <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template> - </action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/bigWigInfo</file> + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="boost" version="1.53.0" /> + </repository> </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> - </package> - - - <package name="deepTools" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc"> - <install version="1.0"> - <actions> - - <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action> - <action type="shell_command">git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc</action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin - </action> - + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> + <action type="shell_command">cd c++ && ./configure --with-boost=$BOOST_ROOT_DIR --prefix=$INSTALL_DIR && make && make install</action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> </action> - </actions> - </install> - <readme>Installation of deepTools from Fidel Ramirez.</readme> - </package> + </actions> + </install> + <readme> +Downloads and compiles BLAST+ from the NCBI, which assumes you have +all the required build dependencies installed. See: +http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download + </readme> + </package> </tool_dependency>