Mercurial > repos > iuc > package_stringtie_1_1_0

changeset 0:62a98ebf406f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
author iuc
date Wed, 21 Oct 2015 16:06:33 -0400
parents
children 4e8dc3ecc62f
files tool_dependencies.xml
diffstat 1 files changed, 50 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 21 16:06:33 2015 -0400
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="stringtie" version="1.1.0">
+      <install version="1.0">
+          <actions_group>
+              <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url" sha256sum="a457dbfee8f66204b17401ac1c4f3c67896ab77f142bad5ac555bfec0d59f613">
+                        http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.1.0.Linux_x86_64.tar.gz
+                    </action>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url" sha256sum="2ccd09274e9c5be1121e55950e6510d7c62a0994266ebfce784c1f493a6c5719">
+                        http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.1.0.OSX_x86_64.tar.gz
+                    </action>
+                    <action type="move_file">
+                      <source>stringtie</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <actions>
+                    <action type="download_by_url" sha256sum="75178e57620abec8e3e544f0430a5f1cdd7fc5faa484fadd8318b5dce90b4fb7">
+                        http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.1.0.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>
+                  <environment_variable action="set_to" name="STRINGTIE_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+  StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
+  It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and
+  quantitate full-length transcripts representing multiple splice variants for each gene locus.
+  Its input can include not only the alignments of raw reads used by other transcript assemblers,
+  but also alignments longer sequences that have been assembled from those reads.
+  To identify differentially expressed genes between experiments, StringTie's
+  output can be processed either by the Cuffdiff or Ballgown programs.
+        </readme>
+    </package>
+</tool_dependency>