diff tool_dependencies.xml @ 0:2c039fc73f1f draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jan 27 09:06:15 2015 -0500
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="perl" version="5.18.1">
+      <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="0.12.7">
+      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="vienna_rna" version="1.8.5">
+      <repository changeset_revision="54e961ee33d4" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pdf_api2" version="2.023">
+      <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="mirdeep2_quantifier" version="2.0">
+      <install version="1.0">
+          <actions>
+              <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action>
+                <action type="move_file">
+                  <source>quantifier.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>make_html2.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>convert_bowtie_output.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+
+The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. 
+First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. 
+By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. 
+The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
+
+        </readme>
+    </package>
+</tool_dependency>