diff tool_dependencies.xml @ 101:4235fcb5b090 draft

Uploaded

--- a/tool_dependencies.xml	Sun Feb 16 06:16:54 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 02 11:49:08 2014 -0500
@@ -1,32 +1,31 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="ncurses" version="5.9">
-        <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="readline" version="6.2">
-        <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="rpy2" version="2.2.3.6">
-        <repository changeset_revision="191967e6496b" name="package_rpy2_2_3_6" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7.1">
-        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="R_statistic_tools" version="1.0">
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="MICLIP_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="miclip" version="1.2">
         <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
                     <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="R_3_0_1" version="3.0.1" />
                     </repository>
-                    <package>https://github.com/bgruening/download_store/raw/master/r_statistic_tools/kernlab_0.9-19.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/r_statistic_tools/yacca_1.1.tar.gz</package>
-                    <package>https://github.com/bgruening/download_store/raw/master/r_statistic_tools/car_2.0-19.tar.gz</package>
+                        <package>https://github.com/bgruening/download_store/raw/master/miclip/moments_0.13.tar.gz</package>
+                        <package>https://github.com/bgruening/download_store/raw/master/miclip/VGAM_0.9-3.tar.gz</package>
+                        <package>https://github.com/bgruening/download_store/raw/master/miclip/MiClip_1.2.tar.gz</package>
                 </action>
             </actions>
         </install>
+        <readme>
+        MiClip: A Model-based Approach to Identify Binding Sites in CLIP-Seq Data
+        Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data.
+        http://cran.r-project.org/web/packages/MiClip/
+        </readme>
     </package>
 </tool_dependency>