Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

comparison tool_dependencies.xml @ 2:b7385e84a15b draft

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planemo upload commit 4abfa4aaee08afe2a3246420ce5d131e1c1d42d8
author mvdbeek
date Fri, 25 Sep 2015 11:31:58 -0400
parents 531f4eea4196
children 69288de0e2f4
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1:531f4eea4196 2:b7385e84a15b
7 <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="sra_toolkit" version="2.5.2"> 9 <package name="sra_toolkit" version="2.5.2">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions> 11 <actions>
12 <action target_filename="sra-tools-2.5.2.tar.gz" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
12 <action type="set_environment_for_install"> 13 <action type="set_environment_for_install">
13 <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 14 <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
14 <package name="ncbi_vdb" version="2.5.2" /> 15 <package name="ncbi_vdb" version="2.5.2" />
15 </repository> 16 </repository>
16 <repository changeset_revision="f530f97e76ea" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 17 <repository changeset_revision="b0e9867f0dfb" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
17 <package name="ngs_sdk" version="1.1.3" /> 18 <package name="ngs_sdk" version="1.1.3" />
18 </repository> 19 </repository>
19 </action> 20 </action>
20 <action target_filename="sra-tools-2.5.2.tar.gz" type="download_file">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> 21 <action type="autoconf">
21 <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action> 22 --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
22 <action type="change_directory">sra-tools-2.5.2</action>
23 <action type="shell_command">
24 ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
25 sed -i -e "109s/-static//" tools/copycat/Makefile
26 </action> 23 </action>
24 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
27 <action type="make_install" /> 25 <action type="make_install" />
28 <action type="shell_command">
29 $INSTALL_DIR/bin/vdb-config --restore-defaults
30 </action>
31 <action type="set_environment"> 26 <action type="set_environment">
32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
33 </action> 28 </action>
34 </actions> 29 </actions>
35 </install> 30 </install>