| Previous changeset 0:4409903dcb88 (2016-01-25) Next changeset 2:fc29c04c3605 (2016-02-18) |
|
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 |
|
modified:
computeGCBias.xml deepTools_macros.xml readme.rst test-data/bamCompare_result2.bw test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result4.bw test-data/bamPEFragmentSize_result1.txt test-data/bigwigCompare_result1.bw test-data/computeMatrix2.bed test-data/computeMatrix2.bw test-data/correctGCBias_result1.bam test-data/plotCoverage_result1.png test-data/plotCoverage_result1.tabular test-data/sequence.2bit test-data/test.bw tool-data/deepTools_seqs.loc.sample tool_dependencies.xml |
|
added:
deepTools_macros.xml.orig static/images/GC_bias_simulated_reads_2L.png static/images/QC_plotCoverage.png static/images/bamCompare_output.png static/images/bamCoverage_output.png static/images/bamPEFragmentSize_output.png static/images/bigwigCompare_output.png static/images/computeGCBias_output.png static/images/computeMatrix_advancedOutput.png static/images/computeMatrix_output.png static/images/computeMatrix_overview.png static/images/computeMatrix_selectRegions.png static/images/computeMatrix_selectScores.png static/images/multiBamSummary_output.png static/images/multiBigwigSummary_output.png static/images/plotCorrelate_RNAseq.png static/images/plotCorrelation_output.png static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png static/images/plotCoverage_annotated.png static/images/plotCoverage_output.png static/images/plotFingerprint_output.png static/images/plotHeatmap_example.png static/images/plotHeatmap_example02.png static/images/plotPCA_annotated.png static/images/plotProfiler_examples.png tool_dependencies.xml.orig |
|
removed:
static/images/flowChart_computeMatrixetc.png |
| b |
| diff -r 4409903dcb88 -r e74853730716 computeGCBias.xml --- a/computeGCBias.xml Mon Jan 25 20:20:49 2016 -0500 +++ b/computeGCBias.xml Mon Feb 15 10:29:47 2016 -0500 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="deeptools_compute_gc_bias" name="computeGCBias" version="@WRAPPER_VERSION@.0"> - <description>to see whether your samples should be normalized for GC bias</description> + <description>Determine the GC bias of your sequenced reads</description> <macros> <token name="@BINARY@">computeGCBias</token> <import>deepTools_macros.xml</import> @@ -126,41 +126,58 @@ </tests> <help> <![CDATA[ -**What it does** +What it does +------------------ This tool computes the GC bias using the method proposed in Benjamini and Speed (2012) Nucleic Acids Res. (see below for further details). -The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias. -There are two plots produced by the tool: a boxplot showing the absolute read numbers per GC-content bin and an x-y plot -depicting the ratio of observed/expected reads per GC-content bin. +The output is used to plot the results and can also be used later on to correct the bias with the tool ``correctGCbias``. +There are two plots produced by the tool: a boxplot showing the absolute read numbers per GC-content bin and an x-y plot depicting the ratio of observed/expected reads per GC-content bin. + +Output files +-------------- ------ +- Diagnostic plots: + - box plot of absolute read numbers per GC-content bin + - x-y plot of observed/expected read ratios per GC-content bin + +- Tabular file: to be used for GC correction with ``correctGCbias`` -**Summary of the method used** +.. image:: $PATH_TO_IMAGES/computeGCBias_output.png + :width: 600 + :height: 455 + +--------------------------------------------- -In order to estimate how many reads with what kind of GC content one should have sequenced, we first need to determine how many regions the -reference genome contains with each percentage of GC content, i.e. how many regions in the genome have 50% GC (or 10% GC or 90% GC or...). -We then sample a large number of equally sized genomic bins and count how many times we see a bin with 50% GC (or 10% GC or 90% or...). These EXPECTED values are independent of any -sequencing bias and is purely dependent on the underlying genome (i.e. it will most likely vary between mouse and fruit fly due to their genome's different GC contents). -The OBSERVED values are based on the reads from the sequenced sample. Instead of noting how many genomic regions there are per GC content, we now count the reads per GC content. -In an ideal sample without GC bias, the ratio of OBSERVED/EXPECTED values should be close to 1 regardless of the GC content. Due to PCR (over)amplifications, the majority of ChIP samples -usually shows a significant bias towards reads with high GC content (>50%) +Background +------------- + +``computeGCBias`` is based on a paper by `Benjamini and Speed <http://nar.oxfordjournals.org/content/40/10/e72>`_. +The basic assumption of the GC bias diagnosis is that an ideal sample should show a uniform distribution of sequenced reads across the genome, i.e. all regions of the genome should have similar numbers of reads, regardless of their base-pair composition. +In reality, the DNA polymerases used for PCR-based amplifications during the library preparation of the sequencing protocols prefer GC-rich regions. This will influence the outcome of the sequencing as there will be more reads for GC-rich regions just because of the DNA polymerase's preference. + +``computeGCbias`` will first calculate the **expected GC profile** by counting the number of DNA fragments of a fixed size per GC fraction where GC fraction is defined as the number of G's or C's in a genome region of a given length. +The result is basically a histogram depicting the frequency of DNA fragments for each type of genome region with a GC fraction between 0 to 100 percent. This will be different for each reference genome, but is independent of the actual sequencing experiment. + +The profile of the expected DNA fragment distribution is then compared to the **observed GC profile**, which is generated by counting the number of sequenced reads per GC fraction. + +In an ideal experiment, the observed GC profile would, of course, look like the expected profile. +This is indeed the case when applying ``computeGCBias`` to simulated reads. + +.. _computeGCBias_example_image: + +.. image:: $PATH_TO_IMAGES/GC_bias_simulated_reads_2L.png + +As you can see, both plots based on **simulated reads** do not show enrichments or depletions for specific GC content bins, there is an almost flat line around the log2ratio of 0 (= ratio(observed/expected) of 1). The fluctuations on the ends of the x axis are due to the fact that only very, very few regions in the *Drosophila* genome have such extreme GC fractions so that the number of fragments that are picked up in the random sampling can vary. + +Now, let's have a look at **real-life data** from genomic DNA sequencing. Panels A and B can be clearly distinguished and the major change that took place between the experiments underlying the plots was that the samples in panel A were prepared with too many PCR cycles and a standard polymerase whereas the samples of panel B were subjected to very few rounds of amplification using a high fidelity DNA polymerase. .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png - - -You can find more details on the computeGCBias doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeGCBias.html - - -**Output files**: + :width: 600 + :height: 452 -- Diagnostic plot +**Note:** The expected GC profile depends on the reference genome as different organisms have very different GC contents. For example, one would expect more fragments with GC fractions between 30% to 60% in mouse samples (average GC content of the mouse genome: 45 %) than for genome fragments from, for example, *Plasmodium falciparum* (average genome GC content *P. falciparum*: 20%). - - box plot of absolute read numbers per GC-content bin - - x-y plot of observed/expected read ratios per GC-content bin - -- Data matrix - - - to be used for GC correction with correctGCbias +For more details, for example about when to exclude regions from the read distribution calculation, go `here <http://deeptools.readthedocs.org/en/latest/content/tools/computeGCBias.html#excluding-regions-from-the-read-distribution-calculation>`_ ----- |
| b |
| diff -r 4409903dcb88 -r e74853730716 deepTools_macros.xml --- a/deepTools_macros.xml Mon Jan 25 20:20:49 2016 -0500 +++ b/deepTools_macros.xml Mon Feb 15 10:29:47 2016 -0500 |
| [ |
| @@ -72,12 +72,12 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.0.1</token> + <token name="@WRAPPER_VERSION@">2.1.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.0.1">deepTools</requirement> + <requirement type="package" version="2.1.0">deepTools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -104,6 +104,7 @@ <param name="clustering_options" type="select" label="Clustering algorithm"> <option value="none">No clustering</option> <option value="kmeans">Kmeans clustering</option> + <option value="hclust">Hierarchical clustering</option> </param> <when value="kmeans"> <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" @@ -112,6 +113,15 @@ If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software."/> </when> + <when value="hclust"> + <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." + help="WARNING: This option causes the tool to run for a very long time! When this option is + set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. + This only works for data that is not grouped, otherwise only the first group will be clustered. + Note that you must have used the '--missingDataAsZero' option within computeMatrix! + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> <when value="none" /> </conditional> </when> @@ -126,6 +136,11 @@ --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans #end if #end if + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': + #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: + --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust + #end if + #end if #end if </token> @@ -293,6 +308,12 @@ </xml> <xml name="multiple_input_bams"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help="The BAM file must be sorted."/> + </xml> + + <xml name="multiple_input_bams_min2"> <param argument="--bamfiles" type="data" format="bam" min="2" label="Bam file" multiple="true" help="The BAM file must be sorted."/> @@ -310,6 +331,7 @@ help="Title of the plot, to be printed on top of the generated image." /> </xml> + <token name="@multiple_input_bams@"> <![CDATA[ #set files=[] |
| b |
| diff -r 4409903dcb88 -r e74853730716 deepTools_macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml.orig Mon Feb 15 10:29:47 2016 -0500 |
| b |
| b'@@ -0,0 +1,639 @@\n+<macros>\n+\n+ <xml name="advancedOpt_scaffold">\n+ <conditional name="advancedOpt">\n+ <param name="showAdvancedOpt" type="select" label="Show advanced options" >\n+ <option value="no" selected="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <yield/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <token name="@ADVANCED_OPTS_READ_PROCESSING@">\n+ #if $advancedOpt.doExtendCustom.doExtend == \'custom\':\n+ --extendReads $advancedOpt.doExtendCustom.extendReadsValue\n+ #else if $advancedOpt.doExtendCustom.doExtend == \'yes\':\n+ --extendReads\n+ #end if\n+ $advancedOpt.ignoreDuplicates\n+ $advancedOpt.centerReads\n+ #if $advancedOpt.minMappingQuality:\n+ --minMappingQuality \'$advancedOpt.minMappingQuality\'\n+ #end if\n+ #if $advancedOpt.samFlagInclude:\n+ --samFlagInclude $advancedOpt.samFlagInclude\n+ #end if\n+ #if $advancedOpt.samFlagExclude:\n+ --samFlagExclude $advancedOpt.samFlagExclude\n+ #end if\n+ </token>\n+\n+ <xml name="heatmap_options">\n+ <expand macro="zMin_zMax" />\n+ <expand macro="colorMap" />\n+ <expand macro="plotTitle" />\n+ <expand macro="plotNumbers" />\n+ </xml>\n+\n+ <token name="@HEATMAP_OPTIONS@">\n+ #if str($plotting_type.zMin) != "":\n+ --zMin $plotting_type.zMin\n+ #end if\n+ #if str($plotting_type.zMax) != "":\n+ --zMax $plotting_type.zMax\n+ #end if\n+ --colorMap \'$plotting_type.colorMap\'\n+ $plotting_type.plotNumbers\n+ --plotTitle \'$plotting_type.plotTitle\'\n+ </token>\n+\n+\n+ <xml name="includeZeros">\n+ <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""\n+ label="Include zeros"\n+ help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />\n+ </xml>\n+\n+ <xml name="zMin_zMax">\n+ <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+ help="If not specified the value is set automatically."/>\n+ <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+ help="If not specified the value is set automatically."/>\n+ </xml>\n+\n+ <xml name="region_limit_operation">\n+ <param argument="--region" type="text" value=""\n+ label="Region of the genome to limit the operation to"\n+ help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />\n+ </xml>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+<<<<<<< HEAD\n+ <token name="@WRAPPER_VERSION@">2.0.1.0</token>\n+=======\n+ <token name="@WRAPPER_VERSION@">2.1.0</token>\n+>>>>>>> d56067f86089e75354a2fad266002db3730766d9\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="2.7.10">python</requirement>\n+ <requirement type="binary">@BINARY@</requirement>\n+<<<<<<< HEAD\n+ <requirement type="package" version="2.0.1">deepTools</requirement>\n+=======\n+ <requirement type="package" version="2.1.0">deepTools</requirement>\n+>>>>>>> d56067f86089e75354a2fad266002db3730766d9\n+ <yield />\n+ </requirements>\n+ <expand macro="stdio" />\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="smoothLength">\n+ <param argument="--smoothLength" type="integer" value="" optional="True" min="1"\n+ label="Smooth values using the following length (in bases)"\n+ help '..b'k2 reversed</option>\n+ <option value="Reds_r">Reds reversed</option>\n+ <option value="Oranges_r">Oranges reversed</option>\n+ <option value="Greens_r">Greens reversed</option>\n+ <option value="Blues_r">Blues reversed</option>\n+ <option value="Greys_r">Greys reversed</option>\n+ <option value="Purples_r">Purples reversed</option>\n+ <option value="Paired_r">Paired reversed</option>\n+ <option value="Pastel1_r">Pastel1 reversed</option>\n+ <option value="Pastel2_r">Pastel2 reversed</option>\n+ <option value="spring_r">spring reversed</option>\n+ <option value="summer_r">summer reversed</option>\n+ <option value="autumn_r">autumn reversed</option>\n+ <option value="winter_r">winter reversed</option>\n+ <option value="hot_r">hot reversed</option>\n+ <option value="coolwarm_r">coolwarm reversed</option>\n+ <option value="cool_r">cool reversed</option>\n+ <option value="seismic_r">seismic reversed</option>\n+ <option value="terrain_r">terrain reversed</option>\n+ <option value="ocean_r">ocean reversed</option>\n+ <option value="rainbow_r">rainbow reversed</option>\n+ <option value="bone_r">bone reversed</option>\n+ <option value="flag_r">flag reversed</option>\n+ <option value="prism_r">prism reversed</option>\n+ <option value="cubehelix_r">cubehelix reversed</option>\n+ <option value="binary_r">binary reversed</option>\n+ <option value="pink_r">pink reversed</option>\n+ <option value="gray_r">gray reversed</option>\n+ <option value="copper_r">copper reversed</option>\n+ <option value="BrBG_r">BrBG reversed</option>\n+ <option value="BuGn_r">BuGn reversed</option>\n+ <option value="BuPu_r">BuPu reversed</option>\n+ <option value="GnBu_r">GnBu reversed</option>\n+ <option value="OrRd_r">OrRd reversed</option>\n+ <option value="PiYG_r">PiYG reversed</option>\n+ <option value="PRGn_r">PRGn reversed</option>\n+ <option value="PuOr_r">PuOr reversed</option>\n+ <option value="PuRd_r">PuRd reversed</option>\n+ <option value="PuBu_r">PuBu reversed</option>\n+ <option value="RdBu_r">RdBu reversed</option>\n+ <option value="RdGy_r">RdGy reversed</option>\n+ <option value="RdPu_r">RdPu reversed</option>\n+ <option value="YlGn_r">YlGn reversed</option>\n+ <option value="PuBuGn_r">PuBuGn reversed</option>\n+ <option value="RdYlBu_r">RdYlBu reversed</option>\n+ <option value="RdYlGn_r">RdYlGn reversed</option>\n+ <option value="YlGnBu_r">YlGnBu reversed</option>\n+ <option value="YlOrBr_r">YlOrBr reversed</option>\n+ <option value="YlOrRd_r">YlOrRd reversed</option>\n+ <option value="gist_gray_r">gist_gray reversed</option>\n+ <option value="gist_stern_r">gist_stern reversed</option>\n+ <option value="gist_earth_r">gist_earth reversed</option>\n+ <option value="gist_yarg_r">gist_yarg reversed</option>\n+ <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ </param>\n+\n+ </xml>\n+\n+</macros>\n' |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/GC_bias_simulated_reads_2L.png |
| b |
| Binary file static/images/GC_bias_simulated_reads_2L.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/QC_plotCoverage.png |
| b |
| Binary file static/images/QC_plotCoverage.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/bamCompare_output.png |
| b |
| Binary file static/images/bamCompare_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/bamCoverage_output.png |
| b |
| Binary file static/images/bamCoverage_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/bamPEFragmentSize_output.png |
| b |
| Binary file static/images/bamPEFragmentSize_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/bigwigCompare_output.png |
| b |
| Binary file static/images/bigwigCompare_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/computeGCBias_output.png |
| b |
| Binary file static/images/computeGCBias_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/computeMatrix_advancedOutput.png |
| b |
| Binary file static/images/computeMatrix_advancedOutput.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/computeMatrix_output.png |
| b |
| Binary file static/images/computeMatrix_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/computeMatrix_overview.png |
| b |
| Binary file static/images/computeMatrix_overview.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/computeMatrix_selectRegions.png |
| b |
| Binary file static/images/computeMatrix_selectRegions.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/computeMatrix_selectScores.png |
| b |
| Binary file static/images/computeMatrix_selectScores.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/flowChart_computeMatrixetc.png |
| b |
| Binary file static/images/flowChart_computeMatrixetc.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/multiBamSummary_output.png |
| b |
| Binary file static/images/multiBamSummary_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/multiBigwigSummary_output.png |
| b |
| Binary file static/images/multiBigwigSummary_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotCorrelate_RNAseq.png |
| b |
| Binary file static/images/plotCorrelate_RNAseq.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotCorrelation_output.png |
| b |
| Binary file static/images/plotCorrelation_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png |
| b |
| Binary file static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotCoverage_annotated.png |
| b |
| Binary file static/images/plotCoverage_annotated.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotCoverage_output.png |
| b |
| Binary file static/images/plotCoverage_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotFingerprint_output.png |
| b |
| Binary file static/images/plotFingerprint_output.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotHeatmap_example.png |
| b |
| Binary file static/images/plotHeatmap_example.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotHeatmap_example02.png |
| b |
| Binary file static/images/plotHeatmap_example02.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotPCA_annotated.png |
| b |
| Binary file static/images/plotPCA_annotated.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 static/images/plotProfiler_examples.png |
| b |
| Binary file static/images/plotProfiler_examples.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/bamCompare_result2.bw |
| b |
| Binary file test-data/bamCompare_result2.bw has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/bamCoverage_result1.bw |
| b |
| Binary file test-data/bamCoverage_result1.bw has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/bamCoverage_result2.bw |
| b |
| Binary file test-data/bamCoverage_result2.bw has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/bamCoverage_result4.bw |
| b |
| Binary file test-data/bamCoverage_result4.bw has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon Jan 25 20:20:49 2016 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 15 10:29:47 2016 -0500 |
| b |
| @@ -2,19 +2,19 @@ Fragment lengths: -Min.: 241 +Min.: 241.0 1st Qu.: 241.5 Mean: 244.666666667 Median: 242.0 3rd Qu.: 246.5 -Max.: 251 +Max.: 251.0 Std: 4.49691252108 Read lengths: -Min.: 251 +Min.: 251.0 1st Qu.: 251.0 Mean: 251.0 Median: 251.0 3rd Qu.: 251.0 -Max.: 251 +Max.: 251.0 Std: 0.0 |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/bigwigCompare_result1.bw |
| b |
| Binary file test-data/bigwigCompare_result1.bw has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/correctGCBias_result1.bam |
| b |
| Binary file test-data/correctGCBias_result1.bam has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/plotCoverage_result1.png |
| b |
| Binary file test-data/plotCoverage_result1.png has changed |
| b |
| diff -r 4409903dcb88 -r e74853730716 test-data/plotCoverage_result1.tabular --- a/test-data/plotCoverage_result1.tabular Mon Jan 25 20:20:49 2016 -0500 +++ b/test-data/plotCoverage_result1.tabular Mon Feb 15 10:29:47 2016 -0500 |
| b |
| b"@@ -1,16570 +1,16570 @@\n-'bowtie2-test1.bam'\t'bowtie2-test1.bam'\n-23\t23\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-27\t27\n-25\t25\n-24\t24\n-21\t21\n-20\t20\n-19\t19\n-19\t19\n-19\t19\n-17\t17\n-17\t17\n-15\t15\n-15\t15\n-15\t15\n-10\t10\n-7\t7\n-7\t7\n-7\t7\n-7\t7\n-6\t6\n-5\t5\n-5\t5\n-5\t5\n-3\t3\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n"..b'\t16415\t16416\t0.0\t0.0\n+chrM\t16416\t16417\t0.0\t0.0\n+chrM\t16417\t16418\t0.0\t0.0\n+chrM\t16418\t16419\t0.0\t0.0\n+chrM\t16419\t16420\t0.0\t0.0\n+chrM\t16420\t16421\t0.0\t0.0\n+chrM\t16421\t16422\t0.0\t0.0\n+chrM\t16422\t16423\t0.0\t0.0\n+chrM\t16423\t16424\t0.0\t0.0\n+chrM\t16424\t16425\t0.0\t0.0\n+chrM\t16425\t16426\t0.0\t0.0\n+chrM\t16426\t16427\t0.0\t0.0\n+chrM\t16427\t16428\t0.0\t0.0\n+chrM\t16428\t16429\t0.0\t0.0\n+chrM\t16429\t16430\t0.0\t0.0\n+chrM\t16430\t16431\t0.0\t0.0\n+chrM\t16431\t16432\t0.0\t0.0\n+chrM\t16432\t16433\t0.0\t0.0\n+chrM\t16433\t16434\t0.0\t0.0\n+chrM\t16434\t16435\t0.0\t0.0\n+chrM\t16435\t16436\t0.0\t0.0\n+chrM\t16436\t16437\t0.0\t0.0\n+chrM\t16437\t16438\t0.0\t0.0\n+chrM\t16438\t16439\t0.0\t0.0\n+chrM\t16439\t16440\t0.0\t0.0\n+chrM\t16440\t16441\t0.0\t0.0\n+chrM\t16441\t16442\t0.0\t0.0\n+chrM\t16442\t16443\t0.0\t0.0\n+chrM\t16443\t16444\t0.0\t0.0\n+chrM\t16444\t16445\t0.0\t0.0\n+chrM\t16445\t16446\t0.0\t0.0\n+chrM\t16446\t16447\t0.0\t0.0\n+chrM\t16447\t16448\t0.0\t0.0\n+chrM\t16448\t16449\t0.0\t0.0\n+chrM\t16449\t16450\t0.0\t0.0\n+chrM\t16450\t16451\t0.0\t0.0\n+chrM\t16451\t16452\t0.0\t0.0\n+chrM\t16452\t16453\t0.0\t0.0\n+chrM\t16453\t16454\t0.0\t0.0\n+chrM\t16454\t16455\t0.0\t0.0\n+chrM\t16455\t16456\t0.0\t0.0\n+chrM\t16456\t16457\t0.0\t0.0\n+chrM\t16457\t16458\t0.0\t0.0\n+chrM\t16458\t16459\t0.0\t0.0\n+chrM\t16459\t16460\t0.0\t0.0\n+chrM\t16460\t16461\t0.0\t0.0\n+chrM\t16461\t16462\t0.0\t0.0\n+chrM\t16462\t16463\t0.0\t0.0\n+chrM\t16463\t16464\t0.0\t0.0\n+chrM\t16464\t16465\t0.0\t0.0\n+chrM\t16465\t16466\t0.0\t0.0\n+chrM\t16466\t16467\t0.0\t0.0\n+chrM\t16467\t16468\t0.0\t0.0\n+chrM\t16468\t16469\t0.0\t0.0\n+chrM\t16469\t16470\t0.0\t0.0\n+chrM\t16470\t16471\t0.0\t0.0\n+chrM\t16471\t16472\t0.0\t0.0\n+chrM\t16472\t16473\t0.0\t0.0\n+chrM\t16473\t16474\t0.0\t0.0\n+chrM\t16474\t16475\t0.0\t0.0\n+chrM\t16475\t16476\t0.0\t0.0\n+chrM\t16476\t16477\t0.0\t0.0\n+chrM\t16477\t16478\t0.0\t0.0\n+chrM\t16478\t16479\t0.0\t0.0\n+chrM\t16479\t16480\t0.0\t0.0\n+chrM\t16480\t16481\t0.0\t0.0\n+chrM\t16481\t16482\t0.0\t0.0\n+chrM\t16482\t16483\t0.0\t0.0\n+chrM\t16483\t16484\t0.0\t0.0\n+chrM\t16484\t16485\t0.0\t0.0\n+chrM\t16485\t16486\t0.0\t0.0\n+chrM\t16486\t16487\t0.0\t0.0\n+chrM\t16487\t16488\t0.0\t0.0\n+chrM\t16488\t16489\t0.0\t0.0\n+chrM\t16489\t16490\t0.0\t0.0\n+chrM\t16490\t16491\t0.0\t0.0\n+chrM\t16491\t16492\t0.0\t0.0\n+chrM\t16492\t16493\t0.0\t0.0\n+chrM\t16493\t16494\t0.0\t0.0\n+chrM\t16494\t16495\t0.0\t0.0\n+chrM\t16495\t16496\t0.0\t0.0\n+chrM\t16496\t16497\t0.0\t0.0\n+chrM\t16497\t16498\t0.0\t0.0\n+chrM\t16498\t16499\t0.0\t0.0\n+chrM\t16499\t16500\t0.0\t0.0\n+chrM\t16500\t16501\t0.0\t0.0\n+chrM\t16501\t16502\t0.0\t0.0\n+chrM\t16502\t16503\t0.0\t0.0\n+chrM\t16503\t16504\t0.0\t0.0\n+chrM\t16504\t16505\t0.0\t0.0\n+chrM\t16505\t16506\t0.0\t0.0\n+chrM\t16506\t16507\t0.0\t0.0\n+chrM\t16507\t16508\t0.0\t0.0\n+chrM\t16508\t16509\t0.0\t0.0\n+chrM\t16509\t16510\t0.0\t0.0\n+chrM\t16510\t16511\t0.0\t0.0\n+chrM\t16511\t16512\t0.0\t0.0\n+chrM\t16512\t16513\t0.0\t0.0\n+chrM\t16513\t16514\t0.0\t0.0\n+chrM\t16514\t16515\t0.0\t0.0\n+chrM\t16515\t16516\t0.0\t0.0\n+chrM\t16516\t16517\t0.0\t0.0\n+chrM\t16517\t16518\t0.0\t0.0\n+chrM\t16518\t16519\t0.0\t0.0\n+chrM\t16519\t16520\t0.0\t0.0\n+chrM\t16520\t16521\t0.0\t0.0\n+chrM\t16521\t16522\t0.0\t0.0\n+chrM\t16522\t16523\t0.0\t0.0\n+chrM\t16523\t16524\t0.0\t0.0\n+chrM\t16524\t16525\t0.0\t0.0\n+chrM\t16525\t16526\t0.0\t0.0\n+chrM\t16526\t16527\t0.0\t0.0\n+chrM\t16527\t16528\t0.0\t0.0\n+chrM\t16528\t16529\t0.0\t0.0\n+chrM\t16529\t16530\t0.0\t0.0\n+chrM\t16530\t16531\t0.0\t0.0\n+chrM\t16531\t16532\t0.0\t0.0\n+chrM\t16532\t16533\t0.0\t0.0\n+chrM\t16533\t16534\t0.0\t0.0\n+chrM\t16534\t16535\t0.0\t0.0\n+chrM\t16535\t16536\t0.0\t0.0\n+chrM\t16536\t16537\t0.0\t0.0\n+chrM\t16537\t16538\t0.0\t0.0\n+chrM\t16538\t16539\t0.0\t0.0\n+chrM\t16539\t16540\t0.0\t0.0\n+chrM\t16540\t16541\t0.0\t0.0\n+chrM\t16541\t16542\t0.0\t0.0\n+chrM\t16542\t16543\t0.0\t0.0\n+chrM\t16543\t16544\t0.0\t0.0\n+chrM\t16544\t16545\t0.0\t0.0\n+chrM\t16545\t16546\t0.0\t0.0\n+chrM\t16546\t16547\t0.0\t0.0\n+chrM\t16547\t16548\t0.0\t0.0\n+chrM\t16548\t16549\t0.0\t0.0\n+chrM\t16549\t16550\t0.0\t0.0\n+chrM\t16550\t16551\t0.0\t0.0\n+chrM\t16551\t16552\t0.0\t0.0\n+chrM\t16552\t16553\t0.0\t0.0\n+chrM\t16553\t16554\t0.0\t0.0\n+chrM\t16554\t16555\t0.0\t0.0\n+chrM\t16555\t16556\t0.0\t0.0\n+chrM\t16556\t16557\t0.0\t0.0\n+chrM\t16557\t16558\t0.0\t0.0\n+chrM\t16558\t16559\t0.0\t0.0\n+chrM\t16559\t16560\t0.0\t0.0\n+chrM\t16560\t16561\t0.0\t0.0\n+chrM\t16561\t16562\t0.0\t0.0\n+chrM\t16562\t16563\t0.0\t0.0\n+chrM\t16563\t16564\t0.0\t0.0\n+chrM\t16564\t16565\t0.0\t0.0\n+chrM\t16565\t16566\t0.0\t0.0\n+chrM\t16566\t16567\t0.0\t0.0\n+chrM\t16567\t16568\t0.0\t0.0\n+chrM\t16568\t16569\t0.0\t0.0\n' |
| b |
| diff -r 4409903dcb88 -r e74853730716 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 25 20:20:49 2016 -0500 +++ b/tool_dependencies.xml Mon Feb 15 10:29:47 2016 -0500 |
| b |
| @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7.10"> - <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="deepTools" version="2.0.1"> - <repository changeset_revision="1fb61fa32733" name="package_python_2_7_deeptools_2_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="deepTools" version="2.1.0"> + <repository changeset_revision="2c54c7c38299" name="package_python_2_7_deeptools_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
| b |
| diff -r 4409903dcb88 -r e74853730716 tool_dependencies.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml.orig Mon Feb 15 10:29:47 2016 -0500 |
| [ |
| @@ -0,0 +1,76 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool_dependency> + <package name="numpy" version="1.9"> + <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" /> + </package> + <package name="pybigwig" version="0.2.4"> + <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc" prior_installation_required="True"/> + </package> + <package name="matplotlib" version="1.4"> + <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" /> + </package> + <package name="scipy" version="0.14"> + <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" /> + </package> +<<<<<<< HEAD + <package name="deepTools" version="2.0.1"> + <repository name="package_python_2_7_deeptools_2_0_1" owner="iuc"/> +======= + <package name="pysam" version="0.8.3"> + <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" /> + </package> + <package name="bx-python" version="0.7.2"> + <repository name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" /> + </package> + <package name="python" version="2.7.10"> + <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" /> +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + </package> + <package name="deepTools" version="2.1.0"> + <install version="1.0"> + <actions> + <action type="setup_python_environment"> + <repository name="package_python_2_7_10" owner="iuc"> + <package name="python" version="2.7.10" /> + </repository> + <repository name="package_python_2_7_pysam_0_8_3" owner="iuc"> + <package name="pysam" version="0.8.3" /> + </repository> + <repository name="package_python_2_7_numpy_1_9" owner="iuc"> + <package name="numpy" version="1.9" /> + </repository> + <repository name="package_python_2_7_matplotlib_1_4" owner="iuc"> + <package name="matplotlib" version="1.4" /> + </repository> + <repository name="package_python_2_7_scipy_0_14" owner="iuc"> + <package name="scipy" version="0.14" /> + </repository> + <repository name="package_python_2_7_bx_python_0_7" owner="iuc"> + <package name="bx-python" version="0.7.2" /> + </repository> + <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc"> + <package name="pybigwig" version="0.2.4" /> + </repository> + <package sha256sum="3bf835afde02cd5247198db3e01f690899e1fdb86e1821a83ac940d807baa857">https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz</package> + </action> + + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> + <!-- libpng lib path --> + <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable> + <!-- disable the config file of deepTools --> + <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable> + </action> + </actions> + </install> + <readme> + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + </readme> + </package> +</tool_dependency> |
