Mercurial > repos > iuc > package_samtools_1_2
diff tool_dependencies.xml @ 10:a55970300738 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 97a064489364118d108b0dd2cfb4d9bc53080837
| author | iuc |
|---|---|
| date | Thu, 19 Nov 2015 14:29:19 -0500 |
| parents | 192f00129358 |
| children | 5b7172f9b230 |
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--- a/tool_dependencies.xml Fri Oct 09 05:22:33 2015 -0400 +++ b/tool_dependencies.xml Thu Nov 19 14:29:19 2015 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="ncurses" version="5.9"> - <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d5587dda75ff" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="zlib" version="1.2.8"> <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> @@ -10,7 +10,7 @@ <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> + <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2%2Bgx1-Linux-x86_64.tar.gz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> @@ -19,7 +19,7 @@ <actions> <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> <action type="set_environment_for_install"> - <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="d5587dda75ff" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="ncurses" version="5.9" /> </repository> <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> @@ -29,11 +29,20 @@ <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> - <action type="shell_command">make</action> + <action type="make_install" /> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> + <action type="shell_command">cd htslib-1.2.1 && make bgzip tabix</action> + <action type="move_file"> + <source>htslib-1.2.1/bgzip</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>htslib-1.2.1/tabix</source> + <destination>$INSTALL_DIR/bin</destination> + </action> </actions> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>