Mercurial > repos > devteam > package_emboss_5_0_0

comparison tool_dependencies.xml @ 7:27b61d58dfb4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded tool dependency definition that attempts to download a platform-specific precompiled binary.
author devteam
date Tue, 10 Dec 2013 11:28:18 -0500
parents 64b58c8f2827
children 27daa4034544
comparison
equal deleted inserted replaced
6:64b58c8f2827 7:27b61d58dfb4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="libx11" version="1.5.0">
4 <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="libxproto" version="7.0.23">
7 <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="libxcb" version="1.9.1">
10 <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="emboss" version="5.0.0"> 3 <package name="emboss" version="5.0.0">
13 <install version="1.0"> 4 <install version="1.0">
14 <actions> 5 <actions_group>
15 <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action> 6 <actions architecture="i386" os="linux">
16 <action type="set_environment_for_install"> 7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/emboss/emboss-5.0.0-Linux-i686.tgz</action>
17 <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> 8 <action type="move_directory_files">
18 <package name="libx11" version="1.5.0" /> 9 <source_directory>.</source_directory>
19 </repository> 10 <destination_directory>$INSTALL_DIR</destination_directory>
20 <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> 11 </action>
21 <package name="libxproto" version="7.0.23" /> 12 </actions>
22 </repository> 13 <actions architecture="x86_64" os="linux">
23 <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> 14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/emboss/emboss-5.0.0-Linux-x86_64.tgz</action>
24 <package name="libxcb" version="1.9.1" /> 15 <action type="move_directory_files">
25 </repository> 16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 </actions>
20 <actions architecture="x86_64" os="darwin">
21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/emboss/emboss-5.0.0-Darwin-x86_64.tgz</action>
22 <action type="move_directory_files">
23 <source_directory>.</source_directory>
24 <destination_directory>$INSTALL_DIR</destination_directory>
25 </action>
26 </actions>
27 <actions>
28 <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action>
29 <action type="set_environment_for_install">
30 <repository changeset_revision="6367d6fc9f82" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
31 <package name="libx11" version="1.5.0" />
32 </repository>
33 <repository changeset_revision="fd9ca3b78488" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
34 <package name="libxproto" version="7.0.23" />
35 </repository>
36 <repository changeset_revision="30193f711b44" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
37 <package name="libxcb" version="1.9.1" />
38 </repository>
39 </action>
40 <action type="shell_command">
41 export LDFLAGS="-L$XCB_LIBS -lm"
42 export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
43 </action>
44 <action type="shell_command">make &amp;&amp; make install</action>
45 <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
46 <action type="change_directory">PHYLIP-3.6b</action>
47 <action type="shell_command">
48 export LDFLAGS="-L$XCB_LIBS -lm"
49 export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
50 </action>
51 <action type="shell_command">make &amp;&amp; make install</action>
52 </actions>
53 <action type="set_environment">
54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
55 <environment_variable action="set_to" name="EMBOSS_ACDROOT">$INSTALL_DIR/share/EMBOSS/acd</environment_variable>
56 <environment_variable action="set_to" name="EMBOSS_DATA">$INSTALL_DIR/share/EMBOSS/data</environment_variable>
57 <environment_variable action="set_to" name="PLPLOT_LIB">$INSTALL_DIR/share/EMBOSS</environment_variable>
26 </action> 58 </action>
27 <action type="shell_command"> 59 </actions_group>
28 export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; \
29 export LDFLAGS="-L$XCB_LIBS" &amp;&amp; \
30 ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
31 </action>
32 <action type="shell_command">make &amp;&amp; make install</action>
33 <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
34 <action type="change_directory">PHYLIP-3.6b</action>
35 <action type="shell_command">
36 export CFLAGS="-I$XPROTO_INCLUDES" &amp;&amp; \
37 export LDFLAGS="-L$XCB_LIBS" &amp;&amp; \
38 ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
39 </action>
40 <action type="shell_command">make &amp;&amp; make install</action>
41 <action type="set_environment">
42 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
43 </action>
44 </actions>
45 </install> 60 </install>
46 <readme> 61 <readme>
47 These links provide information for building the Emboss package in most environments. 62 These links provide information for building the Emboss package in most environments.
48 63
49 System requirements 64 System requirements