Mercurial > repos > iuc > package_samtools_1_2

comparison tool_dependencies.xml @ 9:192f00129358 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
author iuc
date Fri, 09 Oct 2015 05:22:33 -0400
parents 9cd278d52bb6
children a55970300738
comparison
equal deleted inserted replaced
8:9cd278d52bb6 9:192f00129358
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>$INSTALL_DIR</destination_directory>
17 </action>
18 </actions>
12 <actions> 19 <actions>
13 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> 20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
14 <action type="set_environment_for_install"> 21 <action type="set_environment_for_install">
15 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 22 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
16 <package name="ncurses" version="5.9" /> 23 <package name="ncurses" version="5.9" />
18 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 25 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
19 <package name="zlib" version="1.2.8" /> 26 <package name="zlib" version="1.2.8" />
20 </repository> 27 </repository>
21 </action> 28 </action>
22 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> 29 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
23 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action> 30 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action>
24 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> 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$NCURSES_LIB_PATH|g" Makefile</action>
25 <action type="shell_command">make</action> 32 <action type="shell_command">make</action>
26 <action type="move_file"> 33 <action type="move_file">
27 <source>samtools</source> 34 <source>samtools</source>
28 <destination>$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>htslib-1.2.1/bgzip</source>
33 <destination>$INSTALL_DIR/bin</destination>
34 </action>
35 <action type="move_file">
36 <source>htslib-1.2.1/tabix</source>
37 <destination>$INSTALL_DIR/bin</destination> 35 <destination>$INSTALL_DIR/bin</destination>
38 </action> 36 </action>
39 </actions> 37 </actions>
40 <action type="set_environment"> 38 <action type="set_environment">
41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>