Mercurial > repos > jjohnson > package_cap3_3

changeset 0:8b91ecadabb5 draft default tip

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Uploaded
author jjohnson
date Fri, 08 Nov 2013 16:00:56 -0500
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 77 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 08 16:00:56 2013 -0500
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+<tool_dependency>
+    <package name="cap3" version="3">
+        <install version="1.0">
+            <actions_group>
+                <!-- Download the binaries for CAP3 compatible with 64-bit OSX. -->
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url">http://seq.cs.iastate.edu/CAP3/cap3.macosx.intel64.tar</action>
+                    <action type="move_file">
+                        <source>cap3</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>formcon</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for CAP3 compatible with 32-bit OSX. -->
+                <actions os="darwin" architecture="i386">
+                    <action type="download_by_url">http://seq.cs.iastate.edu/CAP3/cap3.macosx.intel32.tar</action>
+                    <action type="move_file">
+                        <source>cap3</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>formcon</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for CAP3 compatible with 64-bit Linux. -->
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url">http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar</action>
+                    <action type="move_file">
+                        <source>cap3</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>formcon</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for CAP3 compatible with 32-bit Linux (i386). -->
+                <actions os="linux" architecture="i386">
+                    <action type="download_by_url">http://seq.cs.iastate.edu/CAP3/cap3.linux.tar</action>
+                    <action type="move_file">
+                        <source>cap3</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>formcon</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
+                <actions>
+                    <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action>
+                    <action type="shell_command">echo Your machine details (the output from 'uname' and 'arch'):</action>
+                    <action type="shell_command">uname</action>
+                    <action type="shell_command">arch</action>
+                    <action type="shell_command">false</action>
+    <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
+                </actions>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+CAP3: A DNA sequence assembly program.
+Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877.
+http://seq.cs.iastate.edu/
+
+LICENCE:
+CAP3 and PCAP are available for use at company under a licensing agreement from Michigan Tech. For information on a licensing agreement, please contact Robin Kolehmainen by email at rakolehm@mtu.edu or by phone at 906-487-2228. Michigan Tech handles licensing agreements on PCAP for Iowa State. 
+
+        </readme>
+    </package>
+</tool_dependency>