Mercurial > repos > iuc > package_samtools_1_2

comparison tool_dependencies.xml @ 7:8d3a21e43004 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
author iuc
date Mon, 29 Jun 2015 14:42:37 -0400
parents 82fe61f0f4a3
children 9cd278d52bb6
comparison
equal deleted inserted replaced
6:82fe61f0f4a3 7:8d3a21e43004
7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="samtools" version="1.2"> 9 <package name="samtools" version="1.2">
10 <install version="1.0"> 10 <install version="1.0">
11 <actions_group> 11 <actions_group>
12 <actions architecture="x86_64" os="linux">
13 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action>
14 <action type="move_directory_files">
15 <source_directory>.</source_directory>
16 <destination_directory>$INSTALL_DIR</destination_directory>
17 </action>
18 </actions>
19 <actions> 12 <actions>
20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> 13 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
21 <action type="set_environment_for_install"> 14 <action type="set_environment_for_install">
22 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 15 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
23 <package name="ncurses" version="5.9" /> 16 <package name="ncurses" version="5.9" />
30 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action> 23 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action>
31 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> 24 <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$NCURSES_LIB_PATH|g" Makefile</action>
32 <action type="shell_command">make</action> 25 <action type="shell_command">make</action>
33 <action type="move_file"> 26 <action type="move_file">
34 <source>samtools</source> 27 <source>samtools</source>
28 <destination>$INSTALL_DIR/bin</destination>
29 </action>
30 <action type="shell_command">cd htslib-1.2.1 &amp;&amp; make bgzip tabix</action>
31 <action type="move_file">
32 <source>bgzip</source>
33 <destination>$INSTALL_DIR/bin</destination>
34 </action>
35 <action type="move_file">
36 <source>tabix</source>
35 <destination>$INSTALL_DIR/bin</destination> 37 <destination>$INSTALL_DIR/bin</destination>
36 </action> 38 </action>
37 </actions> 39 </actions>
38 <action type="set_environment"> 40 <action type="set_environment">
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>