# HG changeset patch
# User mvdbeek
# Date 1434919716 14400
# Node ID 4895f7c6ae4debc62a059d7c43b2a35b0fa7b9ce
# Parent  eee9701a7491c3c1269f8f6c43ed3c7a4a9f4110
planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r eee9701a7491 -r 4895f7c6ae4d readmap.xml
--- a/readmap.xml	Sun Mar 29 13:07:57 2015 -0400
+++ b/readmap.xml	Sun Jun 21 16:48:36 2015 -0400
@@ -1,13 +1,11 @@
-<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.0">
+<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.1">
   <description>from sRbowtie aligment</description>
   <requirements>
         <requirement type="package" version="0.12.7">bowtie</requirement>
         <requirement type="package" version="0.1.18">samtools</requirement>
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="2.14">biocbasics</requirement>
-        <requirement type="package" version="3.0.3">R</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
-        <requirement type="package" version="0.14">scipy</requirement>
   </requirements>
 <command interpreter="python">
         readmap.py 
diff -r eee9701a7491 -r 4895f7c6ae4d smRtools.py
--- a/smRtools.py	Sun Mar 29 13:07:57 2015 -0400
+++ b/smRtools.py	Sun Jun 21 16:48:36 2015 -0400
@@ -4,7 +4,8 @@
 import sys, subprocess
 from collections import defaultdict
 from numpy import mean, median, std
-from scipy import stats
+##Disable scipy import temporarily, as no working scipy on toolshed.
+##from scipy import stats
 
 def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"):
   '''This function will return a dictionary containing fasta identifiers as keys and the
@@ -273,6 +274,8 @@
 
   def correlation_mapper (self, reference, window_size):
     '''to map correlation with a sliding window 26-2-2013'''
+    from scipy import stats
+
     if window_size > self.size:
       return []
     F=open(reference, "r")
diff -r eee9701a7491 -r 4895f7c6ae4d tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 29 13:07:57 2015 -0400
+++ b/tool_dependencies.xml	Sun Jun 21 16:48:36 2015 -0400
@@ -9,37 +9,10 @@
     <package name="pysam" version="0.7.7">
       <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="R" version="3.0.3">
-      <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
-      <install version="1.0">
-          <actions>
-              <action type="set_environment_for_install">
-                  <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                      <package name="R" version="3.0.3" />
-                    </repository>
-                </action>
-                <action type="make_directory">$INSTALL_DIR</action>
-                <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "installme=c(\"lattice\",\"latticeExtra\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "install.packages(c(\"gridBase\",\"gridExtra\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
-            </actions>
-        </install>
-    <package name="numpy" version="1.9">
-        <repository name="package_numpy_1_9" owner="iuc" prior_installation_required="True" />
-    </package>
-    <package name="scipy" version="0.14">
-        <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True" />
-    </package>
-        <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra for managing lattice panels
-        It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
-        Note we use cran at fred hutch since no fastest mirror thingy
-       </readme>
+        <repository changeset_revision="cd2113c820f7" name="package_biocbasics" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>