Mercurial > repos > iuc > package_samtools_1_2

comparison tool_dependencies.xml @ 1:f6ae3ba3f3c1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
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>