Mercurial > repos > iuc > package_sra_toolkit_2_5_2
changeset 1:bb51af9130ea draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
author | iuc |
---|---|
date | Tue, 01 Mar 2016 07:09:32 -0500 |
parents | ab06c0240705 |
children | |
files | tool_dependencies.xml |
diffstat | 1 files changed, 11 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Sun Dec 06 09:04:27 2015 -0500 +++ b/tool_dependencies.xml Tue Mar 01 07:09:32 2016 -0500 @@ -1,10 +1,13 @@ <?xml version="1.0"?> <tool_dependency> <package name="perl" version="5.18.1"> - <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="03f5951a9855" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libmagic" version="5.25"> + <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ncbi_vdb" version="2.5.2"> - <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="17ae6c0040ea" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="ngs_sdk" version="1.1.3"> <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -14,10 +17,13 @@ <actions> <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> <action type="set_environment_for_install"> - <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="03f5951a9855" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="perl" version="5.18.1" /> </repository> - <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libmagic" version="5.25" /> + </repository> + <repository changeset_revision="17ae6c0040ea" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="ncbi_vdb" version="2.5.2" /> </repository> <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> @@ -25,10 +31,7 @@ </repository> </action> <action type="shell_command"> - ./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=$INSTALL_DIR/build - </action> - <action type="shell_command"> - sed -i -e "109s/-static//" tools/copycat/Makefile + ./configure --prefix=$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 </action> <action type="make_install" /> <action type="set_environment">