Mercurial > repos > iuc > package_samtools_1_2

comparison tool_dependencies.xml @ 10:a55970300738 draft

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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
comparison
equal deleted inserted replaced
9:192f00129358 10:a55970300738
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="ncurses" version="5.9"> 3 <package name="ncurses" version="5.9">
4 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="d5587dda75ff" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="zlib" version="1.2.8"> 6 <package name="zlib" version="1.2.8">
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"> 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> 13 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2%2Bgx1-Linux-x86_64.tar.gz</action>
14 <action type="move_directory_files"> 14 <action type="move_directory_files">
15 <source_directory>.</source_directory> 15 <source_directory>.</source_directory>
16 <destination_directory>$INSTALL_DIR</destination_directory> 16 <destination_directory>$INSTALL_DIR</destination_directory>
17 </action> 17 </action>
18 </actions> 18 </actions>
19 <actions> 19 <actions>
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="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 22 <repository changeset_revision="d5587dda75ff" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.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="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">
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.bak -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.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$NCURSES_LIB_PATH|g" Makefile</action> 31 <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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>$INSTALL_DIR/bin</destination>
36 </action>
37 <action type="shell_command">cd htslib-1.2.1 &amp;&amp; make bgzip tabix</action>
38 <action type="move_file">
39 <source>htslib-1.2.1/bgzip</source>
40 <destination>$INSTALL_DIR/bin</destination>
41 </action>
42 <action type="move_file">
43 <source>htslib-1.2.1/tabix</source>
35 <destination>$INSTALL_DIR/bin</destination> 44 <destination>$INSTALL_DIR/bin</destination>
36 </action> 45 </action>
37 </actions> 46 </actions>
38 <action type="set_environment"> 47 <action type="set_environment">
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>