Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

comparison tool_dependencies.xml @ 5:aabb60d93e4a draft

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planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
author mvdbeek
date Fri, 25 Sep 2015 13:18:52 -0400
parents 9b27d2331ce2
children 9a412e6be961
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4:9b27d2331ce2 5:aabb60d93e4a
2 <tool_dependency> 2 <tool_dependency>
3 <package name="ascp" version="3"> 3 <package name="ascp" version="3">
4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="ncbi_vdb" version="2.5.2"> 6 <package name="ncbi_vdb" version="2.5.2">
7 <repository changeset_revision="a20af718e248" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="9e86738381d1" 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>
13 <action type="set_environment_for_install"> 12 <action type="set_environment_for_install">
14 <repository changeset_revision="a20af718e248" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 13 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
15 <package name="ncbi_vdb" version="2.5.2" /> 14 <package name="ncbi_vdb" version="2.5.2" />
16 </repository> 15 </repository>
17 <repository changeset_revision="c9b972613908" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 16 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="ngs_sdk" version="1.1.3" /> 17 <package name="ngs_sdk" version="1.1.3" />
19 </repository> 18 </repository>
20 </action> 19 </action>
21 <action type="autoconf"> 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>
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=$INSTALL_DIR/build 21 <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action>
22 <action type="change_directory">sra-tools-2.5.2</action>
23 <action type="shell_command">
24 ./configure --prefix=$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
23 </action> 26 </action>
24 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
25 <action type="make_install" /> 27 <action type="make_install" />
28 <action type="shell_command">
29 $INSTALL_DIR/bin/vdb-config --restore-defaults
30 </action>
26 <action type="set_environment"> 31 <action type="set_environment">
27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
28 </action> 33 </action>
29 </actions> 34 </actions>
30 </install> 35 </install>