# HG changeset patch
# User mvdbeek
# Date 1434916788 14400
# Node ID 9f75d887904d3f9ea794e66797c122ea0fb833ae
# Parent 6c72cf9a00dfd4f34d54e8c7370e6b16055acc54
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
diff -r 6c72cf9a00df -r 9f75d887904d size_histogram.xml
--- a/size_histogram.xml Sun Mar 29 12:54:10 2015 -0400
+++ b/size_histogram.xml Sun Jun 21 15:59:48 2015 -0400
@@ -4,10 +4,9 @@
bowtie
samtools
pysam
+ R
biocbasics
- R
numpy
- scipy
size_histogram.py
diff -r 6c72cf9a00df -r 9f75d887904d smRtools.py
--- a/smRtools.py Sun Mar 29 12:54:10 2015 -0400
+++ b/smRtools.py Sun Jun 21 15:59:48 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 6c72cf9a00df -r 9f75d887904d smRtools.pyc
Binary file smRtools.pyc has changed
diff -r 6c72cf9a00df -r 9f75d887904d tool_dependencies.xml
--- a/tool_dependencies.xml Sun Mar 29 12:54:10 2015 -0400
+++ b/tool_dependencies.xml Sun Jun 21 15:59:48 2015 -0400
@@ -9,37 +9,10 @@
-
-
+
+
-
-
-
-
-
-
-
- $INSTALL_DIR
- echo "bioclite=\"http://bioconductor.org/biocLite.R\"" > $INSTALL_DIR/runme.R
- echo "source(bioclite)" >> $INSTALL_DIR/runme.R
- echo "installme=c(\"lattice\",\"latticeExtra\")" >> $INSTALL_DIR/runme.R
- echo "biocLite()" >> $INSTALL_DIR/runme.R
- echo "biocLite(installme)" >> $INSTALL_DIR/runme.R
- echo "install.packages(c(\"gridBase\",\"gridExtra\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" >> $INSTALL_DIR/runme.R
- echo "quit(save=\"no\")" >> $INSTALL_DIR/runme.R
- export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R
-
-
-
-
-
-
-
-
- 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
-
+