Mercurial > repos > matt-shirley > sra_tools
diff tool_dependencies.xml @ 47:04cc8176e86f draft default tip
update to SRA toolkit 2.3.3-3
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 16 Sep 2013 20:27:28 -0400 |
| parents | 88a13a2fd23f |
| children |
line wrap: on
line diff
--- a/tool_dependencies.xml Tue Sep 03 22:02:30 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 16 20:27:28 2013 -0400 @@ -1,18 +1,18 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sra_toolkit" version="2.3.2-4"> + <package name="sra_toolkit" version="2.3.3-3"> <install version="1.0"> <actions> - <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action> - <action type="shell_command">make release</action> - <action type="shell_command">make static</action> - <action type="shell_command">make</action> - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="make_directory">$INSTALL_DIR/ncbi</action> - <action type="make_directory">$INSTALL_DIR/ncbi/public</action> - <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> - <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> - <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> + <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</action> + <action type="shell_command">make release</action> + <action type="shell_command">make static</action> + <action type="shell_command">make</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/ncbi</action> + <action type="make_directory">$INSTALL_DIR/ncbi/public</action> + <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action> + <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action> + <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action> </actions> </install> <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.