Mercurial > repos > iuc > package_sra_toolkit_2_5_2

comparison tool_dependencies.xml @ 2:163cf5b7c14e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 1c0647ec605bc15e0a749833c37f2cf2c5bc69b4
author iuc
date Tue, 01 Mar 2016 03:06:46 -0500
parents 2255f3e3cbb3
children b1bf5fd340ca
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1:2255f3e3cbb3 2:163cf5b7c14e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="perl" version="5.18.1"> 3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="318ccddfe301" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="libmagic" version="5.25">
7 <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 8 </package>
6 <package name="ncbi_vdb" version="2.5.2"> 9 <package name="ncbi_vdb" version="2.5.2">
7 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 11 </package>
9 <package name="ngs_sdk" version="1.1.3"> 12 <package name="ngs_sdk" version="1.1.3">
12 <package name="sra_toolkit" version="2.5.2"> 15 <package name="sra_toolkit" version="2.5.2">
13 <install version="1.0"> 16 <install version="1.0">
14 <actions> 17 <actions>
15 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> 18 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
16 <action type="set_environment_for_install"> 19 <action type="set_environment_for_install">
17 <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 20 <repository changeset_revision="318ccddfe301" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="perl" version="5.18.1" /> 21 <package name="perl" version="5.18.1" />
22 </repository>
23 <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="libmagic" version="5.25" />
19 </repository> 25 </repository>
20 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 26 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 <package name="ncbi_vdb" version="2.5.2" /> 27 <package name="ncbi_vdb" version="2.5.2" />
22 </repository> 28 </repository>
23 <repository changeset_revision="1381744a8a09" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 29 <repository changeset_revision="1381744a8a09" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="ngs_sdk" version="1.1.3" /> 30 <package name="ngs_sdk" version="1.1.3" />
25 </repository> 31 </repository>
26 </action> 32 </action>
27 <action type="shell_command"> 33 <action type="shell_command">
28 ./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=$INSTALL_DIR/build 34 ./configure --prefix=$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
29 </action>
30 <action type="shell_command">
31 sed -i -e "109s/-static//" tools/copycat/Makefile
32 </action> 35 </action>
33 <action type="make_install" /> 36 <action type="make_install" />
34 <action type="set_environment"> 37 <action type="set_environment">
35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
36 </action> 39 </action>