Mercurial > repos > iuc > package_stringtie_1_0_1

changeset 0:cd94bd10219b draft default tip

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Uploaded tool dependency definition.
author iuc
date Thu, 05 Mar 2015 10:52:50 -0500
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 41 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Mar 05 10:52:50 2015 -0500
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="stringtie" version="1.0.1">
+      <install version="1.0">
+          <actions_group>
+              <actions architecture="x86_64" os="linux">
+                  <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.0.1.Linux_x86_64.tar.gz</action>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                  <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.0.1.OSX_x86_64.tar.gz</action>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <actions>
+                  <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.0.1.tar.gz</action>
+                    <action type="shell_command">make release</action>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>StringTie is a fast and highly efficient assembler of RNA-Seq
+        alignments into potential transcripts. It is primarily a genome-guided
+        transcriptome assembler, although it can borrow algorithmic techniques
+        from de novo genome assembly to help with transcript assembly. Its input
+        can include not only the spliced read alignments used by reference-based
+        assemblers, but also longer contigs that were assembled de novo from
+        unambiguous, non-branching parts of a transcript.</readme>
+    </package>
+</tool_dependency>