Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
changeset 1:eee9701a7491 draft
Uploaded
author | mvdbeek |
---|---|
date | Sun, 29 Mar 2015 13:07:57 -0400 |
parents | 9af9983dcd02 |
children | 4895f7c6ae4d |
files | readmap.xml runme.R tool_dependencies.xml |
diffstat | 3 files changed, 26 insertions(+), 23 deletions(-) [+] |
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--- a/readmap.xml Mon Nov 03 10:28:40 2014 -0500 +++ b/readmap.xml Sun Mar 29 13:07:57 2015 -0400 @@ -6,8 +6,9 @@ <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> - <parallelism method="basic"></parallelism> <command interpreter="python"> readmap.py #if $refGenomeSource.genomeSource == "history": @@ -258,23 +259,27 @@ :width: 500 </help> - + <tests> <test> <param name="genomeSource" value="history" /> <param name="ownFile" value ="transposons.fasta" ftype="fasta" /> - <param name="input" value="sample1.srbowtie_out, sample2.srbowtie_out, sample3.srbowtie_out" ftype="tabular" /> - <param name="norm" value="1,1,1" /> + <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/> + <param name="series_0|norm" value="1" /> + <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/> + <param name="series_1|norm" value="1" /> + <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/> + <param name="series_2|norm" value="1" /> <param name="minquery" value="20" /> <param name="maxquery" value="30" /> <param name="title" value="Readmaps and size distributions" /> <param name="xlabel" value="Coordinates/read size" /> <param name="ylabel" value="Number of reads" /> <param name="rows_per_page" value="8" /> - <output name="readmap_dataframe" ftype="tabular" value="Readmap_dataframe.tab" /> - <output name="size_distribution_dataframe" ftype="tabular" value="Size_distribution_dataframe.tab" /> - <output name="readmap_PDF" ftype="pdf" value="Readmaps.pdf" /> - <output name="size_PDF" ftype="pdf" value="Size_distribution.pdf" /> - <output name="combi_PDF" ftype="pdf" value="Size_distribution_and_Readmaps.pdf" /> + <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" /> + <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" /> + <output name="readmap_PDF" ftype="pdf" file="Readmaps.pdf" /> + <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" /> + <output name="combi_PDF" ftype="pdf" file="Size_distribution_and_Readmaps.pdf" /> </test> - + </tests> </tool>
--- a/runme.R Mon Nov 03 10:28:40 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -bioclite = "http://bioconductor.org/biocLite.R" -install.packages(c("lattice","latticeExtra"),dependencies=T,repos=http://cran.us.r-project.org) -source(bioclite) -installme=c(lattice,latticeExtra) -biocLite() -biocLite(installme) -quit(save="no") -
--- a/tool_dependencies.xml Mon Nov 03 10:28:40 2014 -0500 +++ b/tool_dependencies.xml Sun Mar 29 13:07:57 2015 -0400 @@ -1,22 +1,22 @@ <?xml version="1.0"?> <tool_dependency> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="bowtie" version="0.12.7"> + <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="pysam" version="0.7.7"> - <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <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="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e509651776fa" name="package_r_3_0_3" 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="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <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> @@ -31,6 +31,12 @@ <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