# HG changeset patch # User bgruening # Date 1422050011 18000 # Node ID f3140d17939eb405d91f0d6596ce1bee2723defe # Parent c699d2b577f851544d7cebe934dfe0b657e1e81c Uploaded diff -r c699d2b577f8 -r f3140d17939e bamCompare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCompare.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,221 @@ + + normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig) + + + + bamCompare + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e bamCorrelate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCorrelate.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,206 @@ + + correlates pairs of BAM files + + + + bamCorrelate + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveRawCounts'] is True + )) + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveCorMatrix'] is True + )) + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e bamCoverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCoverage.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,198 @@ + + generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig) + + + + bamCoverage + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e bamFingerprint.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamFingerprint.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,150 @@ + + plots profiles of BAM files; useful for assesing ChIP signal strength + + + + bamFingerprint + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveRawCounts'] is True + )) + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e bamPEFragmentSize.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamPEFragmentSize.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,56 @@ + + Given a BAM file it samples several regions to estimate the paird-end fragment length + + + + bamPEFragmentSize + deepTools_macros.xml + + + $outfile + && + mv ./hist.png $histogram_outfile +]]> + + + + + + + + + histogram is True + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e bigwigCompare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwigCompare.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,133 @@ + + normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference + + + + bigwigCompare + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e computeGCBias.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeGCBias.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,167 @@ + + to see whether your samples should be normalized for GC bias + + + + computeGCBias + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + image_format != 'none' + )) + + + + + + + + + + + + + + + + + + + + + + + +50%) + +.. image:: $PATH_TO_IMAGES/QC_GCplots_input.png + + +You can find more details on the computeGCBias wiki page: computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias + + +**Output files**: + +- Diagnostic plot + + - box plot of absolute read numbers per genomic GC bin + - x-y plot of observed/expected read ratios per genomic GC content bin + +- Data matrix + + - to be used for GC correction with correctGCbias + + +----- + +@REFERENCES@ +]]> + + + diff -r c699d2b577f8 -r f3140d17939e computeMatrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrix.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,269 @@ + + summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile + + + + computeMatrix + deepTools_macros.xml + + +> $temp_input_path; + #if str($rf.label.value).strip(): + echo "\#$rf.label.value" >> $temp_input_path; + #else: + echo "\#$rf.regionsFile.name" >> $temp_input_path; + #end if + #end for + + computeMatrix + + $mode.mode_select + --regionsFileName '$temp_input_path' + --scoreFileName '$scoreFile' + --outFileName '$outFileName' + + @THREADS@ + + #if $output.showOutputSettings == "yes" + #if $output.saveData: + --outFileNameData '$outFileNameData' + #end if + #if $output.saveMatrix: + --outFileNameMatrix '$outFileNameMatrix' + #end if + + #if $output.saveSortedRegions: + --outFileSortedRegions '$outFileSortedRegions' + #end if + #end if + + #if $mode.mode_select == "reference-point": + --referencePoint $mode.referencePoint + $mode.nanAfterEnd + --beforeRegionStartLength $mode.beforeRegionStartLength + --afterRegionStartLength $mode.afterRegionStartLength + #else + --regionBodyLength $mode.regionBodyLength + --startLabel "$mode.startLabel" + --endLabel "$mode.endLabel" + #if $mode.regionStartLength.regionStartLength_select == "yes": + --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength + --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength + #end if + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + --sortRegions '$advancedOpt.sortRegions' + --sortUsing '$advancedOpt.sortUsing' + --averageTypeBins '$advancedOpt.averageTypeBins' + $advancedOpt.missingDataAsZero + $advancedOpt.skipZeros + --binSize $advancedOpt.binSize + + #if $advancedOpt.minThreshold: + --minThreshold $advancedOpt.minThreshold + #end if + #if $advancedOpt.maxThreshold: + --maxThreshold $advancedOpt.maxThreshold + #end if + #if $advancedOpt.scale: + --scale $advancedOpt.scale + #end if + + #end if + ; rm $temp_input_path +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e correctGCBias.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/correctGCBias.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,76 @@ + + uses the output from computeGCBias to generate corrected BAM files + + + + correctGCBias + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e deepTools_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,480 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + --numberOfProcessors "\${GALAXY_SLOTS:-4}" + 1.5.9.1 + + + @BINARY@ + samtools + deepTools + ucsc_tools + python + deepTools + ucsc_tools + numpy + pysam + scipy + matplotlib + samtools + bx-python + + + @BINARY@ --version + + + + + + + + + + + + + + + + + + + + + + + + + + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + +.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ +.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de +.. _help site: https://github.com/fidelram/deepTools/wiki/ + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following paper: + + + + + 10.1093/nar/gku365 + + + + + + + + + + + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) + #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) + #silent $files.append('%s.bam' % $temp_input_path) + + ##set $files += [str($i.bamfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bamfile.name)] + #end if + #end for + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "${source.input1_2bit.fields.path}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveData'] is True + )) + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e heatmapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmapper.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,228 @@ + + creates a heatmap for a score associated to genomic regions + + + + heatmapper + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e profiler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profiler.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,183 @@ + + + creates a profile plot for a score associated to genomic regions + + + + + profiler + deepTools_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value) + + + + + + + + + + + + + + + + + + + + + + diff -r c699d2b577f8 -r f3140d17939e readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,74 @@ +======================== +Galaxy deeptools wrapper +======================== + +deepTools are user-friendly tools for the normalization and visualization of +deep-sequencing data. +They address the challenge of visualizing the large amounts of data that are now +routinely generated from sequencing centers in a meaningful way. +To do so, deepTools contain useful routines to process the mapped reads data +through removal of duplicates and different filtering options to create coverage +files in standard bedGraph and bigWig file formats. deepTools allow the creation +of normalized coverage files or the comparison between two files +(for example, treatment and control). Finally, using such normalized and +standardized files, multiple visualizations can be created to identify +enrichments with functional annotations of the genome. +For a gallery of images that can be produced and a description +of the tools see our poster_. + +.. _poster: http://f1000.com/posters/browse/summary/1094053 + +deeptools is developed under here: + + https://github.com/fidelram/deepTools + +For support, questions, or feature requests contact: deeptools@googlegroups.com + + +============ +Installation +============ + +Requirements: python-2.7 + +Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. + +For the best performance we recommend to install blas/lapack/atlas in your environment before +installing deepTools from the Tool Shed. + + +======== +Citation +======== + +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. + + +======= +History +======= + + * v1.0: Initial public release + * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff -r c699d2b577f8 -r f3140d17939e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,7 @@ + + + + value, name, path + +
+ diff -r c699d2b577f8 -r f3140d17939e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig + + + $INSTALL_DIR/bedGraphToBigWig + + + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo + + + $INSTALL_DIR/bigWigInfo + + + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph + + + $INSTALL_DIR/bigWigToBedGraph + + + $INSTALL_DIR + + + + The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility. + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.9.1.tar.gz + + + + $INSTALL_DIR/bin + $INSTALL_DIR/lib/python + + TRUE + + + + + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + + + diff -r c699d2b577f8 -r f3140d17939e tool_test_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.html Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,356 @@ + + + + + + + Tool Test Results (powered by Planemo) + + + + + + + + + + + + + + +
+
+
+ + +
+
+ +

Overview

+
+
+
+

Tests

+

The remainder of this contains a description for each test executed to run these jobs.

+
+
+
+ + + + + + + diff -r c699d2b577f8 -r f3140d17939e tool_test_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.json Fri Jan 23 16:53:31 2015 -0500 @@ -0,0 +1,1 @@ +{"tests": [{"data": {"status": "failure", "inputs": {"advancedOpt|showAdvancedOpt": "no", "bigwigFile2": {"src": "hda", "id": "2891970512fa2d5a"}, "comparison|comparison_select": "ratio", "outFileFormat": "bigwig", "bigwigFile1": {"src": "hda", "id": "2891970512fa2d5a"}}, "output_problems": ["Job in error state.", "Job in error state."], "job": {"inputs": {"bigwigFile2": {"src": "hda", "id": "2891970512fa2d5a"}, "bigwigFile1": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-01-21T14:00:16.502455", "tool_id": "deeptools_bigwigCompare", "outputs": {"outFileName": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "", "command_line": "bigwigCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat' --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_2.dat' --outFileFormat 'bigwig' --ratio ratio --pseudocount 1.0", "exit_code": 1, "state": "error", "create_time": "2015-01-21T14:00:03.956345", "params": {"comparison": "{\"pseudocount\": \"1.0\", \"__current_case__\": 1, \"comparison_select\": \"ratio\"}", "outFileFormat": "\"bigwig\"", "region": "\"\"", "dbkey": "\"hg17\"", "advancedOpt": "{\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}", "chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "Fatal error: Exit code 1 ()\n\n######################################################\n\nThe program *bedGraphToBigWig* was not found in your PATH. In\norder for deeptools to work properly this program needs\nto be installed. If you already have a copy of this\nprogram please be sure that it is found in your PATH or\nthat is referred in the configuration file of deepTools\nlocated at:\n\n/home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n\nThe program can be downloaded from here:\n http://hgdownload.cse.ucsc.edu/admin/exe/\n\n\n########################################################\n\nThe output is set by default to 'bedgraph'\nsh: 1: bigWigInfo: not found\nsh: 1: bigWigInfo: not found\nError: The generated bedGraphFile was empty. Please adjust\nyour deepTools settings and check your input files.", "job_metrics": [], "model_class": "Job", "external_id": "17230", "id": "5729865256bc2525", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n testMethod()\n File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 223, in test_tool\n self.do_it( td )\n File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 66, in do_it\n raise e\nJobOutputsError: Job in error state.\nJob in error state.\n-------------------- >> begin captured stdout << ---------------------\nHistory with id 2891970512fa2d5a in error - summary of datasets in error below.\n--------------------------------------\n| 2 - bigwigCompare on data 1 (HID - NAME) \n| Dataset Blurb:\n| error\n| Dataset Info:\n| Fatal error: Exit code 1 ()\n| ######################################################\n| The program *bedGraphToBigWig* was not found in your PATH. In\n| order for deeptools to work properly this program needs\n| to be installed. If you already have a copy of this\n| Dataset Job Standard Output:\n| *Standard output was empty.*\n| Dataset Job Standard Error:\n| Fatal error: Exit code 1 ()\n| ######################################################\n| The program *bedGraphToBigWig* was not found in your PATH. In\n| order for deeptools to work properly this program needs\n| to be installed. If you already have a copy of this\n| program please be sure that it is found in your PATH or\n| that is referred in the configuration file of deepTools\n| located at:\n| /home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n| The program can be downloaded from here:\n| http://hgdownload.cse.ucsc.edu/admin/exe/\n| ########################################################\n| The output is set by default to 'bedgraph'\n| sh: 1: bigWigInfo: not found\n| sh: 1: bigWigInfo: not found\n| Error: The generated bedGraphFile was empty. Please adjust\n| your deepTools settings and check your input files.\n|\n--------------------------------------\nHistory with id 2891970512fa2d5a in error - summary of datasets in error below.\n--------------------------------------\n| 2 - bigwigCompare on data 1 (HID - NAME) \n| Dataset Blurb:\n| error\n| Dataset Info:\n| Fatal error: Exit code 1 ()\n| ######################################################\n| The program *bedGraphToBigWig* was not found in your PATH. In\n| order for deeptools to work properly this program needs\n| to be installed. If you already have a copy of this\n| Dataset Job Standard Output:\n| *Standard output was empty.*\n| Dataset Job Standard Error:\n| Fatal error: Exit code 1 ()\n| ######################################################\n| The program *bedGraphToBigWig* was not found in your PATH. In\n| order for deeptools to work properly this program needs\n| to be installed. If you already have a copy of this\n| program please be sure that it is found in your PATH or\n| that is referred in the configuration file of deepTools\n| located at:\n| /home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n| The program can be downloaded from here:\n| http://hgdownload.cse.ucsc.edu/admin/exe/\n| ########################################################\n| The output is set by default to 'bedgraph'\n| sh: 1: bigWigInfo: not found\n| sh: 1: bigWigInfo: not found\n| Error: The generated bedGraphFile was empty. Please adjust\n| your deepTools settings and check your input files.\n|\n--------------------------------------\n\n--------------------- >> end captured stdout << ----------------------\n-------------------- >> begin captured logging << --------------------\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"POST /api/users HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/1\ngalaxy.jobs.handler: DEBUG: (1) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (1) Job dispatched\ngalaxy.jobs.runners: DEBUG: (1) command is: python /home/bag/projects/code/galaxy-central/tools/data_source/upload.py /home/bag/projects/code/galaxy-central /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/tmp/tmpRpbhPM 1:/tmp/tmpPIgGHs/job_working_directory/000/1/dataset_1_files:/tmp/tmpPIgGHsfiles/000/dataset_1.dat; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/1 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/1/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_ccsVhS,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_Qq5BwN,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_WKo1fr,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_cB8OGx,,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_hOnJAL; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/1/galaxy_1.sh\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/1/galaxy_1.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1\ngalaxy.jobs: DEBUG: job 1 ended\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/2\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.handler: INFO: (2) Job dispatched\ngalaxy.jobs.runners: DEBUG: (2) command is: bigwigCompare --version > /tmp/tmpPIgGHs/tmp/GALAXY_VERSION_STRING_2 2>&1; bigwigCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat' --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_2.dat' --outFileFormat 'bigwig' --ratio ratio --pseudocount 1.0; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/2 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/2/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_rw8GcL,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_hap93L,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_fGfc3v,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_IUTLzd,,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_BgsayE; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs.output_checker: INFO: Job 2: Fatal error: Exit code 1 ()\ngalaxy.jobs: DEBUG: setting dataset state to ERROR\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 2 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?full=true&key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_deeptools_bigwigCompare.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"advancedOpt|showAdvancedOpt": "no", "bigwigFile2": {"src": "hda", "id": "54f2a3a23292eb07"}, "comparison|comparison_select": "ratio", "outFileFormat": "bedgraph", "bigwigFile1": {"src": "hda", "id": "54f2a3a23292eb07"}}, "output_problems": ["History item different than expected, difference (using diff):\n( /home/bag/projects/code/deepTools/galaxy/wrapper/test-data/bigwigCompare_result2.bg v. /tmp/tmpPIgGHs/tmp/tmpGqBqc9bigwigCompare_result2.bg )\n--- local_file\n+++ history_data\n@@ -1,5 +0,0 @@\n-chr21\t0\t10000000\t1.0\n-chr21\t10000000\t20000000\t1.0\n-chr21\t20000000\t30000000\t1.0\n-chr21\t30000000\t40000000\t1.0\n-chr21\t40000000\t48129895\t1.0\n"], "job": {"inputs": {"bigwigFile2": {"src": "hda", "id": "54f2a3a23292eb07"}, "bigwigFile1": {"src": "hda", "id": "54f2a3a23292eb07"}}, "update_time": "2015-01-21T14:00:46.256358", "tool_id": "deeptools_bigwigCompare", "outputs": {"outFileName": {"src": "hda", "id": "8155e4b4bf1581ff"}}, "stdout": "", "command_line": "bigwigCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat' --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_4.dat' --outFileFormat 'bedgraph' --ratio ratio --pseudocount 1.0", "exit_code": 0, "state": "ok", "create_time": "2015-01-21T14:00:37.272522", "params": {"comparison": "{\"pseudocount\": \"1.0\", \"__current_case__\": 1, \"comparison_select\": \"ratio\"}", "outFileFormat": "\"bedgraph\"", "region": "\"\"", "dbkey": "\"hg17\"", "advancedOpt": "{\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}", "chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "\n######################################################\n\nThe program *bedGraphToBigWig* was not found in your PATH. In\norder for deeptools to work properly this program needs\nto be installed. If you already have a copy of this\nprogram please be sure that it is found in your PATH or\nthat is referred in the configuration file of deepTools\nlocated at:\n\n/home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n\nThe program can be downloaded from here:\n http://hgdownload.cse.ucsc.edu/admin/exe/\n\n\n########################################################\n\nThe output is set by default to 'bedgraph'\nsh: 1: bigWigInfo: not found\nsh: 1: bigWigInfo: not found\n", "job_metrics": [], "model_class": "Job", "external_id": "17321", "id": "8155e4b4bf1581ff", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n testMethod()\n File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 223, in test_tool\n self.do_it( td )\n File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 66, in do_it\n raise e\nJobOutputsError: History item different than expected, difference (using diff):\n( /home/bag/projects/code/deepTools/galaxy/wrapper/test-data/bigwigCompare_result2.bg v. /tmp/tmpPIgGHs/tmp/tmpGqBqc9bigwigCompare_result2.bg )\n--- local_file\n+++ history_data\n@@ -1,5 +0,0 @@\n-chr21\t0\t10000000\t1.0\n-chr21\t10000000\t20000000\t1.0\n-chr21\t20000000\t30000000\t1.0\n-chr21\t30000000\t40000000\t1.0\n-chr21\t40000000\t48129895\t1.0\n\n-------------------- >> begin captured logging << --------------------\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 3\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/3\ngalaxy.jobs.handler: DEBUG: (3) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (3) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: (3) command is: python /home/bag/projects/code/galaxy-central/tools/data_source/upload.py /home/bag/projects/code/galaxy-central /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/tmp/tmpz8wZrv 3:/tmp/tmpPIgGHs/job_working_directory/000/3/dataset_3_files:/tmp/tmpPIgGHsfiles/000/dataset_3.dat; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/3 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/3/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_M641RK,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_vknCha,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_RHHbx7,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_Scjshu,,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_B79aAL; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/3/galaxy_3.sh\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/3/galaxy_3.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 3\ngalaxy.jobs: DEBUG: job 3 ended\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/4\ngalaxy.jobs.handler: DEBUG: (4) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (4) Job dispatched\ngalaxy.jobs.runners: DEBUG: (4) command is: bigwigCompare --version > /tmp/tmpPIgGHs/tmp/GALAXY_VERSION_STRING_4 2>&1; bigwigCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat' --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_4.dat' --outFileFormat 'bedgraph' --ratio ratio --pseudocount 1.0; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/4 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/4/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/4/metadata_in_HistoryDatasetAssociation_4_ZCW55i,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_kwds_HistoryDatasetAssociation_4_HKOLTz,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_out_HistoryDatasetAssociation_4_aEOFWP,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_results_HistoryDatasetAssociation_4_O_YvpP,,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_override_HistoryDatasetAssociation_4_KJj66T; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (4) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/4/galaxy_4.sh\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/4/galaxy_4.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 4 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?full=true&key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff/display?raw=true&key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpPIgGHs/jobfiles, ofn: /tmp/tmpPIgGHs/jobfiles/bigwigCompare_result2.bg\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpPIgGHs/jobfiles. saved /tmp/tmpPIgGHs/jobfiles/bigwigCompare_result2.bg\nbase.twilltestcase: INFO: ## files diff on /home/bag/projects/code/deepTools/galaxy/wrapper/test-data/bigwigCompare_result2.bg and /tmp/tmpPIgGHs/tmp/tmpGqBqc9bigwigCompare_result2.bg lines_diff=0, found diff = 5\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_deeptools_bigwigCompare.test_tool_000001", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 2, "num_tests": 2}} \ No newline at end of file