Mercurial > repos > devteam > package_emboss_5_0_0

annotate tool_dependencies.xml @ 2:3569b0e8a8c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
author devteam
date Tue, 25 Jun 2013 15:36:12 -0400
parents f117a9d9dc9c
children 0e97d4936c23
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
2 <tool_dependency>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
3 <package name="libx11" version="1.5.0">
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
4 <repository changeset_revision="90c1cbb8095a" name="package_x11_client_1_5_proto_7_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
5 </package>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
6 <package name="emboss" version="5.0.0">
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
7 <install version="1.0">
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
8 <actions>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
9 <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
10 <action type="set_environment_for_install">
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
11 <repository changeset_revision="90c1cbb8095a" name="package_x11_client_1_5_proto_7_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
12 <package name="libx11" version="1.5.0" />
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
13 </repository>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
14 </action>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
15 <action type="shell_command">
2
3569b0e8a8c1 Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
devteam
parents: 1
diff changeset
16 if [ -z $X11_LIB_DIR ] [ -z $X11_INCLUDE_DIR ]; then
0
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
17 ./configure --prefix=$INSTALL_DIR
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
18 else
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
19 ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
20 fi
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
21 </action>
1
f117a9d9dc9c Update the tool_dependencies.xml to use a single <actions> tag set.
devteam
parents: 0
diff changeset
22 <action type="shell_command">make &amp;&amp; make install</action>
f117a9d9dc9c Update the tool_dependencies.xml to use a single <actions> tag set.
devteam
parents: 0
diff changeset
23 <action type="download_file" extract="true">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
f117a9d9dc9c Update the tool_dependencies.xml to use a single <actions> tag set.
devteam
parents: 0
diff changeset
24 <action type="change_directory">PHYLIP-3.6b</action>
0
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
25 <action type="shell_command">
2
3569b0e8a8c1 Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
devteam
parents: 1
diff changeset
26 if [ -z $X11_LIB_DIR ] [ -z $X11_INCLUDE_DIR ]; then
0
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
27 ./configure --prefix=$INSTALL_DIR
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
28 else
1
f117a9d9dc9c Update the tool_dependencies.xml to use a single <actions> tag set.
devteam
parents: 0
diff changeset
29 ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR CFLAGS='-I../include'
0
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
30 fi
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
31 </action>
1
f117a9d9dc9c Update the tool_dependencies.xml to use a single <actions> tag set.
devteam
parents: 0
diff changeset
32 <action type="shell_command">make &amp;&amp; make install</action>
2
3569b0e8a8c1 Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
devteam
parents: 1
diff changeset
33 <action type="set_environment">
3569b0e8a8c1 Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
devteam
parents: 1
diff changeset
34 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
3569b0e8a8c1 Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
devteam
parents: 1
diff changeset
35 </action>
0
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
36 </actions>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
37 </install>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
38 <readme>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
39 These links provide information for building the Emboss package in most environments.
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
40
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
41 System requirements
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
42 http://emboss.sourceforge.net/download/#Requirements
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
43
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
44 Platform-dependent notes
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
45 http://emboss.sourceforge.net/download/#Platforms
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
46 </readme>
9fd501d0f295 Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
devteam
parents:
diff changeset
47 </package>
2
3569b0e8a8c1 Uploaded tool dependency definition that explicitly prepends $INSTALL_DIR/bin to the $PATH environment variable.
devteam
parents: 1
diff changeset
48 </tool_dependency>