Mercurial > repos > mvdbeek > test_sra
diff tool_dependencies.xml @ 2:2c5483e80fb7 draft
planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 14 Aug 2015 12:48:14 -0400 |
| parents | 29892b1d24b9 |
| children | fb21b2e48a1e |
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--- a/tool_dependencies.xml Fri Aug 14 12:29:26 2015 -0400 +++ b/tool_dependencies.xml Fri Aug 14 12:48:14 2015 -0400 @@ -1,15 +1,30 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sra_toolkit" version="2.4.5"> + <package name="sra_toolkit" version="2.5.2"> <install version="1.0"> <actions> <action type="make_directory">src</action> <action type="make_directory">build</action> <action type="change_directory">src</action> + <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> <action type="shell_command"> - git clone https://github.com/mdshw5/sra-tools.git - git clone https://github.com/mdshw5/ncbi-vdb.git - git clone https://github.com/mdshw5/ngs.git + tar -xf 2.5.2.tar.gz + rm 2.5.2.tar.gz + mv sra-tools-2.5.2 sra-tools + </action> + <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action> + <action type="shell_command"> + tar -xf 1.1.3.tar.gz + rm 1.1.3.tar.gz + mv ngs-1.1.3 ngs + </action> + <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action> + <action type="shell_command"> + tar -xf 2.5.2.tar.gz + rm 2.5.2.tar.gz + mv ncbi-vdb-2.5.2 ncbi-vdb + </action> + <action type="shell_command"> LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib cd $INSTALL_DIR/src/ncbi-vdb ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build