Mercurial > repos > iuc > package_samtools_1_2
comparison tool_dependencies.xml @ 1:f6ae3ba3f3c1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
| author | iuc |
|---|---|
| date | Fri, 17 Jul 2015 11:11:30 -0400 |
| parents | 6eea04363026 |
| children |
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| 0:6eea04363026 | 1:f6ae3ba3f3c1 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="ncurses" version="5.9"> | |
| 4 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="zlib" version="1.2.8"> | |
| 7 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 3 <package name="samtools" version="1.2"> | 9 <package name="samtools" version="1.2"> |
| 4 <install version="1.0"> | 10 <install version="1.0"> |
| 5 <actions_group> | 11 <actions_group> |
| 6 <actions architecture="x86_64" os="linux"> | 12 <actions architecture="x86_64" os="linux"> |
| 7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> | 13 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> |
| 9 <source_directory>.</source_directory> | 15 <source_directory>.</source_directory> |
| 10 <destination_directory>$INSTALL_DIR</destination_directory> | 16 <destination_directory>$INSTALL_DIR</destination_directory> |
| 11 </action> | 17 </action> |
| 12 </actions> | 18 </actions> |
| 13 <actions> | 19 <actions> |
| 14 <package name="ncurses" version="5.9"> | |
| 15 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 16 </package> | |
| 17 <package name="zlib" version="1.2.8"> | |
| 18 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 19 </package> | |
| 20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> | 20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> |
| 21 <action type="set_environment_for_install"> | 21 <action type="set_environment_for_install"> |
| 22 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | 22 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 23 <package name="ncurses" version="5.9" /> | 23 <package name="ncurses" version="5.9" /> |
| 24 </repository> | 24 </repository> |
| 25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | 25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 26 <package name="zlib" version="1.2.8" /> | 26 <package name="zlib" version="1.2.8" /> |
| 27 </repository> | 27 </repository> |
| 28 </action> | 28 </action> |
| 29 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> | 29 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> |
| 30 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action> | 30 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> |
| 31 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> | 31 <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> |
| 32 <action type="shell_command">make</action> | 32 <action type="make_install" /> |
| 33 <action type="move_file"> | 33 <action type="move_file"> |
| 34 <source>samtools</source> | 34 <source>samtools</source> |
| 35 <destination>$INSTALL_DIR/bin</destination> | 35 <destination>$INSTALL_DIR/bin</destination> |
| 36 </action> | 36 </action> |
| 37 </actions> | 37 </actions> |