Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

comparison tool_dependencies.xml @ 6:9a412e6be961 draft

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planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
author mvdbeek
date Sun, 25 Oct 2015 18:41:18 -0400
parents aabb60d93e4a
children 5f56355f5f7c
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5:aabb60d93e4a 6:9a412e6be961
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="9e86738381d1" 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="perl" version="5.18.1">
10 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
9 <package name="sra_toolkit" version="2.5.2"> 12 <package name="sra_toolkit" version="2.5.2">
10 <install version="1.0"> 13 <install version="1.0">
11 <actions> 14 <actions>
15 <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"> 16 <action type="set_environment_for_install">
13 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 17 <repository changeset_revision="9e86738381d1" 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" /> 18 <package name="ncbi_vdb" version="2.5.2" />
15 </repository> 19 </repository>
16 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 20 <repository changeset_revision="a00c9a1db096" 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" /> 21 <package name="ngs_sdk" version="1.1.3" />
18 </repository> 22 </repository>
23 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="perl" version="5.18.1" />
25 </repository>
19 </action> 26 </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> 27 <action type="autoconf">
21 <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action> 28 --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> 29 </action>
30 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
27 <action type="make_install" /> 31 <action type="make_install" />
28 <action type="shell_command">
29 $INSTALL_DIR/bin/vdb-config --restore-defaults
30 </action>
31 <action type="set_environment"> 32 <action type="set_environment">
32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
33 </action> 34 </action>
34 </actions> 35 </actions>
35 </install> 36 </install>