Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
changeset 2:4895f7c6ae4d draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | mvdbeek |
|---|---|
| date | Sun, 21 Jun 2015 16:48:36 -0400 |
| parents | eee9701a7491 |
| children | f6dc63230483 |
| files | readmap.xml smRtools.py tool_dependencies.xml |
| diffstat | 3 files changed, 8 insertions(+), 34 deletions(-) [+] |
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--- 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
--- 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")
--- 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\"" > $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "source(bioclite)" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "installme=c(\"lattice\",\"latticeExtra\")" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "install.packages(c(\"gridBase\",\"gridExtra\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">echo "quit(save=\"no\")" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">export PATH=$PATH && 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>