| Next changeset 1:5f69a2c1b9c9 (2016-02-24) |
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Uploaded initial version 0.4.4. |
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added:
README.rst data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml data_manager_conf.xml rnachipintegrator_canonical_genes.xml rnachipintegrator_macros.xml rnachipintegrator_wrapper.sh rnachipintegrator_wrapper.xml test-data/ChIP_peaks.txt test-data/ChIP_summits.txt test-data/ExpressionData.txt test-data/mm9_canonical_genes.data_manager_json test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt test-data/mm9_peaks.xls test-data/mm9_summits.txt test-data/mm9_summits.xls test-data/mm9_summits_to_transcripts.out test-data/mm9_transcripts_to_edges.out test-data/mm9_transcripts_to_edges.summary test-data/mm9_tss_to_edges.out test-data/mm9_tss_to_edges.summary test-data/mm9_tss_to_summits.out test-data/peaks.xls test-data/peaks_to_transcripts.out test-data/rnachipintegrator_canonical_genes.loc test-data/summits.xls test-data/transcripts_to_edges.out test-data/transcripts_to_edges.summary test-data/tss_to_edges.out test-data/tss_to_edges.summary test-data/tss_to_summits.out tool-data/rnachipintegrator_canonical_genes.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r d9c1f2133124 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jun 30 06:44:06 2015 -0400 |
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| @@ -0,0 +1,142 @@ +RnaChipIntegrator: integrated analysis of gene expression and ChIP data +======================================================================= + +Galaxy tool wrappers for running the RnaChipIntegrator program +(http://fls-bioinformatics-core.github.com/RnaChipIntegrator/) for integrated +analyses of gene expression and ChIP data. + +There are two tools available that are built around RnaChipIntegrator: + +- General RnaChipIntegrator tool that allows any peaks to be analysed against + any gene list +- A "cannonical gene" variant which allows ChIP peaks to be analysed against a + list of cannonical genes for different genomes + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take of installing the tool wrapper +and the RnaChipIntegrator programs, installing the .loc files, and setting the +appropriate environment variables. + +Manual Installation +=================== + +There are three files to install: + +- ``rnachipintegrator_wrapper.xml`` (the Galaxy tool definition for general usage) +- ``rnachipintegrator_canonical_genes.xml`` (tool definition for the "canonical + gene" variant) +- ``rnachipintegrator_wrapper.sh`` (the shell script wrapper) + +The suggested location is in a ``tools/rnachipintegrator/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the lines: + + <tool file="rnachipintegrator/rnachipintegrator_wrapper.xml" /> + <tool file="rnachipintegrator/rnachipintegrator_canonical_genes.xml" /> + +You will also need to install the RnaChipIntegrator program: + +- http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ + +In addition for the cannonical gene and histone modification variants, it's +necessary to copy the .loc.sample files to .loc Galaxy's ``tool-data`` folder: + +- **Cannonical genes**: its necessary to manually acquire cannonical gene + list files from UCSC and then add appropriate references in the + ``rnachipintegrator_canonical_genes.loc`` file. + +If you want to run the functional tests, copy the sample test files under +``test-data`` to Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id fls_rnachipintegrator_wrapper + + +How to get canonical gene data +============================== + +Getting canonical gene info from UCSC is covered in the screencast at +http://blog.openhelix.eu/?p=6097 + +In summary: + +- **UCSC genome browser:** if multiple versions of each gene are visible (e.g. + if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000) + then: + + - Scroll down to the Gene & Gene Prediction section + - Click on the UCSC genes link + - Uncheck the tickbox next to splice variants and resubmit to view without + duplicates. + +- **UCSC table browser:** to obtain the canonical set of genes from the table + browser: + + - Select knownCanonical from the table menu + - Select selected fields from primary & related tables from the output format menu + - Click on Get output + - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the + 'knownCanonical' table plus 'geneSymbol' from the kgXref table.) + - Click on Get output to get the data for download + +(Hint: to also get strand direction information i.e. +/-, also allow selection +from the refGene table, and select the strand field.) + + +Note on Excel output files and Galaxy +===================================== + +RnaChipIntegrator produces an Excel spreadsheet as one of its outputs, +however Galaxy is not currently set up by default to handle these. + +To enable Excel output file handling in Galaxy, edit the ``datatypes_conf.xml`` +file and add: + + <datatype extension="xls" type="galaxy.datatypes.data:Data" mimetype="application/vnd.ms-excel" /> + +You'll also need to remove the existing datatype with extension "xls". + +Restarting Galaxy should mean that the browser correctly handles Excel outputs +from RnaChipIntegrator. + +History +======= + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +0.4.4-0 - Initial version pushed to toolshed +========== ====================================================================== + + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_rnachipintegrator_wrapper.sh`` script. + + +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. |
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| diff -r 000000000000 -r d9c1f2133124 data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py Tue Jun 30 06:44:06 2015 -0400 |
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| @@ -0,0 +1,97 @@ +#!/usr/bin/env python +# + +import sys +import os +import optparse +import shutil + +from galaxy.util.json import from_json_string, to_json_string + +# Download file from specified URL and put into local subdir + +if __name__ == '__main__': + #Parse Command Line + parser = optparse.OptionParser() + options,args = parser.parse_args() + print "options: %s" % options + print "args : %s" % args + if len(args) != 2: + p.error("Need to supply JSON file name and description text") + + # Read the JSON supplied from the data manager tool + # Results from this program will be returned via the + # same file + jsonfile = args[0] + params = from_json_string(open(jsonfile).read() ) + print "%s" % params + + # Extract the data from the input JSON + # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29 + # for example of JSON + # + # We want the values set in the data manager XML + dbkey = params['param_dict']['dbkey'] + description = args[1].strip() + identifier = params['param_dict']['unique_id'].strip() + # Where to put the output file + # Nb we have to make this ourselves, it doesn't exist by default + target_dir = params['output_data'][0]['extra_files_path'] + os.mkdir(target_dir) + + method = params['param_dict']['reference_source']['reference_source_selector'] + + # Dictionary for returning to data manager + data_manager_dict = {} + data_manager_dict['data_tables'] = dict() + + if method == 'server': + # Pull in a file from the server + filename = params['param_dict']['reference_source']['gene_list_filename'] + create_symlink = params['param_dict']['reference_source']['create_symlink'] + print "Canonical gene list file name: %s" % filename + print "Create symlink: %s" % create_symlink + target_filename = os.path.join(target_dir,os.path.basename(filename)) + if create_symlink == 'copy_file': + shutil.copyfile(filename,target_filename) + else: + os.symlink(filename,target_filename) + # Check identifier and description + if not description: + description = "%s: %s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + if not identifier: + identifier = "%s_%s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + # Update the output dictionary + data_manager_dict['data_tables']['rnachipintegrator_canonical_genes'] = { + 'value': identifier, + 'dbkey': dbkey, + 'name': description, + 'path': os.path.basename(filename), + } + elif method == 'history': + # Copy file from history + filename = params['param_dict']['reference_source']['input_gene_list'] + target_filename = os.path.join(target_dir,os.path.basename(filename)) + shutil.copyfile(filename,target_filename) + # Check identifier and description + if not description: + description = "%s: %s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + if not identifier: + identifier = "%s_%s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + # Update the output dictionary + data_manager_dict['data_tables']['rnachipintegrator_canonical_genes'] = { + 'value': identifier, + 'dbkey': dbkey, + 'name': description, + 'path': os.path.basename(filename), + } + else: + raise NotImplementedError("Method '%s' not implemented" % method) + + #save info to json file + open(jsonfile,'wb').write(to_json_string(data_manager_dict)) + |
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| diff -r 000000000000 -r d9c1f2133124 data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml Tue Jun 30 06:44:06 2015 -0400 |
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| @@ -0,0 +1,90 @@ +<tool id="data_manager_rnachipintegrator_fetch_canonical_genes" name="Fetch RnaChipIntegrator canonical genes" version="0.0.1" tool_type="manage_data"> + <description>Fetch and install canonical gene lists for RnaChipIntegrator</description> + <command interpreter="python">data_manager_rnachipintegrator_fetch_canonical_genes.py + "${out_file}" + "${description}"</command> + <inputs> + <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> + <param type="text" name="unique_id" label="Internal identifier" + help="Identifier string to associate with the annotation e.g. 'mm9_generic'" /> + <param type="text" name="description" value="" + label="Description of canonical gene list" size="50" + help="Text that will appear in the list of canonical genes" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="history">History</option> + <option value="server">File on the server</option> + </param> + <when value="server"> + <param type="text" name="gene_list_filename" value="" size="50" + label="Full path to the canonical genes file on disk" optional="False" /> + <param type="boolean" name="create_symlink" + truevalue="create_symlink" falsevalue="copy_file" + label="Create symlink to orignal data instead of copying" checked="False" /> + </when> + <when value="history"> + <param name="input_gene_list" type="data" format="tabular" + label="Canonical gene list from history" optional="False" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <param name="dbkey" value="mm9"/> + <param name="description" value="Mouse (mm9)"/> + <param name="reference_source_selector" value="history"/> + <param name="input_gene_list" value="mm9_canonical_genes.tsv"/> + <output name="out_file" file="mm9_canonical_genes.data_manager_json"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +Adds a canonical gene list file to the *rnachipintegrator_canonical_genes* +data table, so that it can be used in the *Analyse canonical genes against ChIP +data* tool. + +At present the gene list files must be created manually and placed on the +Galaxy server; see below for information on how to obtain canonical gene lists +from UCSC. + +**Notice:** If you leave the description blank then it will be generated +automatically. + +------ + +.. class:: infomark + +**Obtaining canonical gene lists** + +Getting canonical gene info from UCSC is covered in the screencast at +http://blog.openhelix.eu/?p=6097 + +**UCSC genome browser:** if multiple versions of each gene are visible (e.g. +if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000) +then: + + - Scroll down to the *Gene & Gene Prediction* section + - Click on the *UCSC genes* link + - Uncheck the tickbox next to *splice variants* and resubmit to view without + duplicates. + +**UCSC table browser:** to obtain the canonical set of genes from the table browser: + + - Select *knownCanonical* from the table menu + - Select selected fields from primary & related tables from the output format menu + - Click on *Get output* + - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the + 'knownCanonical' table plus 'geneSymbol' from the *kgXref* table.) + - Click on Get output to get the data for download + +**Hint:** to also get strand direction information i.e. +/-, also allow selection +from the refGene table, and select the strand field.) + </help> +</tool> |
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| diff -r 000000000000 -r d9c1f2133124 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Jun 30 06:44:06 2015 -0400 |
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| @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml" id="data_manager_rnachipintegrator_fetch_canonical_genes"> + <data_table name="rnachipintegrator_canonical_genes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rnachipintegrator/${dbkey}/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rnachipintegrator/${dbkey}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_canonical_genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_canonical_genes.xml Tue Jun 30 06:44:06 2015 -0400 |
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| b'@@ -0,0 +1,235 @@\n+<tool id="rnachipintegrator_canonical_genes" name="Analyse canonical genes against ChIP data" version="@VERSION@-0">\n+ <description>using RnaChipIntegrator</description>\n+ <macros>\n+ <import>rnachipintegrator_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+ <command interpreter="bash">rnachipintegrator_wrapper.sh\n+ #if str( $analysis_options.peak_type ) == "summits"\n+ #if str( $analysis_options.window ) != ""\n+ --window=$analysis_options.window\n+ #end if\n+ #if str( $analysis_options.cutoff ) != ""\n+ --cutoff=$analysis_options.cutoff\n+ #end if\n+ #end if\n+ #if str( $analysis_options.peak_type ) == "regions"\n+ #if str( $analysis_options.edge_cutoff ) != ""\n+ --edge-cutoff=$analysis_options.edge_cutoff\n+ #end if\n+ #if str( $analysis_options.number ) != ""\n+ --number=$analysis_options.number\n+ #end if\n+ #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end ))\n+ --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end\n+ #end if\n+ #if $analysis_options.pad_output\n+ --pad\n+ #end if\n+ #end if\n+ ${canonical_genes.fields.path} $chipseq\n+ --output_xls $xls_output\n+ #if $results_as_zip\n+ --zip_file $zip_file\n+ #else\n+ #if str( $analysis_options.peak_type ) == "summits"\n+ --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out\n+ #end if\n+ #if str( $analysis_options.peak_type ) == "regions"\n+ --peak_outputs $transcripts_to_edges_out\n+ $transcripts_to_edges_summary\n+ $tss_to_edges_out\n+ $tss_to_edges_summary\n+ #end if\n+ #end if\n+ </command>\n+ <inputs>\n+ <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" />\n+ <param name="canonical_genes" type="select" label="Canonical genes to analyse ChIP peaks against">\n+ <options from_data_table="rnachipintegrator_canonical_genes">\n+ </options>\n+ </param>\n+ <conditional name="analysis_options">\n+ <!-- user must specify if ChIP peaks are summits or regions -->\n+ <param name="peak_type" type="select" label="ChIP peaks are"\n+\t help="Options and outputs depend on whether ChIP data are summits or regions">\n+ <option value="summits">summits</option>\n+ <option value="regions">regions</option>\n+ </param>\n+ <when value="summits">\n+ <param name="window" type="integer" value="20000" optional="true"\n+\t label="Maximum distance a peak can be from each transcript\n+\t\t TSS before being omitted from analysis" />\n+ <param name="cutoff" type="integer" value="130000" optional="true"\n+\t label="Maximum distance a transcript TSS can be from each\n+\t\t peak before being omitted from the analysis" />\n+ </when>\n+ <when value="regions">\n+ <param name="edge_cutoff" type="integer" value="10000" optional="true"\n+\t label="Maximum distance a transcript edge can be from the\n+\t\t peak edge before being omitted from the analysis"\n+\t help="Set to zero to indicate that no cut off should be applied" />\n+ <param name="number" type="integer" value="4" optional="true"\n+\t label="Maximum number of transcripts per peak to report from\n+\t\t from the analysis" />\n+ <param name="promoter_start" type="integer" value="-10000" optional="true"\n+\t label="Start of promoter region with respect to gene TSS" />\n+ <param name="promoter_end" type="integer" value="2500" optional="true"\n+\t label="End of promoter region with respect to gene TSS" />\n+ <param name="pad_output" type="boolean" checked="false" truevalue="yes"\n+\t label="Output same number of lines for each peak (--pad)"\n+\t help="Add blank lines in output for peaks with fewer than maximum number\n+\t\t of hits" />\n+ </when>\n+ </conditional>\n+ <param name="results_as_zip" type="boolean" checked="false" truevalue="yes"\n+ label="Put output tab-delimited '..b'put name="tss_to_summits_out" file="mm9_tss_to_summits.out" ftype="tabular" />\n+ </test>\n+ <test>\n+ <param name="chipseq" value="mm9_peaks.txt" />\n+ <param name="canonical_genes" value="mm9_test" />\n+ <param name="peak_type" value="regions" />\n+ <param name="edge_cutoff" value="50000" />\n+ <output name="xls_output" file="mm9_peaks.xls" compare="sim_size" />\n+ <output name="transcripts_to_edges_out" file="mm9_transcripts_to_edges.out" ftype="tabular" />\n+ <output name="transcripts_to_edges_summary" file="mm9_transcripts_to_edges.summary" ftype="tabular" />\n+ <output name="tss_to_edges_out" file="mm9_tss_to_edges.out" ftype="tabular" />\n+ <output name="tss_to_edges_summary" file="mm9_tss_to_edges.summary" ftype="tabular" />\n+ </test>\n+ </tests>\n+ <help>\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+Run RnaChipIntegrator to analyse ChIP data against a set of list of "canonical\n+genes" for a specific organism/genome build, identifying the nearest ChIP peaks\n+to each cannonical gene (vice versa).\n+\n+For ChIP peaks defined as regions the following analyses are performed:\n+\n+ * **TranscriptsToPeakEdges**: reports the nearest transcripts with the smallest\n+ distance from either their TSS or TES to the nearest peak edge.\n+\n+ * **TSSToPeakEdges**: reports the nearest transcripts with the smallest distance\n+ from their TSS to the nearest peak edge.\n+\n+For ChIP peaks defined as summits:\n+\n+ * **TSSToSummits**: reports the nearest transcripts with the smallest distance\n+ from the TSS to the nearest peak summit.\n+\n+ * **PeaksToTranscripts**: reports the nearest peak summits with the smallest\n+ distance to either the TSS or TES of each transcript.\n+\n+RnaChipIntgerator can be obtained from\n+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+The ChIP-seq data must be in a tab-delimited file with 3 columns of data for each\n+ChIP peak (one per line):\n+\n+====== ========== ======================================================================\n+Column Name Description\n+====== ========== ======================================================================\n+ 1 chr Chromosome name (must match one of those in expression data file)\n+ 2 start Start position of the peak \n+ 3 end End position of the peak (start + 1 for summit data)\n+====== ========== ======================================================================\n+\n+The ChIP peak data can be either the summit (in which case \'end\' - \'start\' = 1) or the\n+entire extent of the binding region (with \'start\' and \'end\' indicating the limits).\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+The outputs from this tool vary depending on the type of ChIP data that is input (i.e\n+summits or peaks), however generally there is one tab-delimited results file for each\n+analysis described above in the **What it does** section (some analyses output a second\n+file with just the "best" hits).\n+\n+A history item will be generated for each output file, unless the option to put them\n+into a single zip archive is selected; this archive file will have to be downloaded\n+and unzipped on your local machine. It is recommended that you refer to the\n+RnaChipIntegrator documentation for information on the contents of each output file:\n+https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown\n+\n+In addition an Excel spreadsheet (with one page for each analysis performed) is always\n+produced.\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Credits**\n+\n+This Galaxy tool has been developed within the Bioinformatics Core Facility at the\n+University of Manchester. It runs the RnaChipIntegrator package which has also been\n+developed by this group, and is documented at\n+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/\n+\n+Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_macros.xml Tue Jun 30 06:44:06 2015 -0400 |
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| @@ -0,0 +1,14 @@ +<macros> + <token name="@VERSION@">0.4.4</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.7.5">python_xlwt</requirement> + <requirement type="package" version="0.9.3">python_xlrd</requirement> + <requirement type="package" version="1.7.1">python_xlutils</requirement> + <requirement type="package" version="0.4.4">rnachipintegrator</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>rnachipintegrator --version</version_command> + </xml> +</macros> |
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| diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_wrapper.sh Tue Jun 30 06:44:06 2015 -0400 |
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| @@ -0,0 +1,137 @@ +#!/bin/sh +# +# Wrapper script to run RnaChipIntegrator as a Galaxy tool +# +# usage: sh rnachipintegrator_wrapper.sh [OPTIONS] <rnaseq_in> <chipseq_in> --output_xls <xls_out> +# +echo RnaChipIntegrator: analyse gene expression and ChIP data +# +# Collect command line options +opts= +output_xls= +peaks_to_transcripts_out= +zip_file= +while [ ! -z "$1" ] ; do + case $1 in + --output_xls) + shift; output_xls=$1 + ;; + --summit_outputs) + shift; peaks_to_transcripts_out=$1 + shift; tss_to_summits_out=$1 + ;; + --peak_outputs) + shift; transcripts_to_edges_out=$1 + shift; transcripts_to_edges_summary=$1 + shift; tss_to_edges_out=$1 + shift; tss_to_edges_summary=$1 + ;; + --zip_file) + shift; zip_file=$1 + ;; + *) + opts="$opts $1" + ;; + esac + shift +done +# +# Run RnaChipIntegrator +# NB append stderr to stdout otherwise Galaxy job will fail +# Direct output to a temporary directory +outdir=`mktemp -d` +base_name=galaxy +cmd="RnaChipIntegrator.py --project=${outdir}/${base_name} $opts" +echo $cmd +$cmd 2>&1 +# +# Check exit code +exit_status=$? +if [ "$exit_status" -ne "0" ] ; then + echo RnaChipIntegrator exited with non-zero status >&2 + # Clean up and exit + /bin/rm -rf $outdir + exit $exit_status +fi +# +# Deal with output files - XLS +if [ -f "${outdir}/${base_name}.xls" ] ; then + /bin/mv ${outdir}/${base_name}.xls $output_xls +else + echo No file ${outdir}/${base_name}.xls >&2 + # Clean up and exit + /bin/rm -rf $outdir + exit 1 +fi +# +# Zip file +if [ ! -z "$zip_file" ] ; then + for ext in "PeaksToTranscripts" "TSSToSummits" "TranscriptsToPeakEdges" "TranscriptsToPeakEdges_summary" "TSSToPeakEdges" "TSSToPeakEdges_summary" ; do + txt_file=${outdir}/${base_name}_${ext}.txt + if [ -f "$txt_file" ] ; then + zip -j -g ${outdir}/archive.zip $txt_file + fi + done + /bin/mv ${outdir}/archive.zip $zip_file +fi +# +# Peaks to transcripts +if [ ! -z "$peaks_to_transcripts_out" ] ; then + outfile=${outdir}/${base_name}_PeaksToTranscripts.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $peaks_to_transcripts_out + else + echo No file $outfile >&2 + fi +fi +# +# TSS to summits +if [ ! -z "$tss_to_summits_out" ] ; then + outfile=${outdir}/${base_name}_TSSToSummits.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $tss_to_summits_out + else + echo No file $outfile >&2 + fi +fi +# +# Transcripts to Peak Edges +if [ ! -z "$transcripts_to_edges_out" ] ; then + outfile=${outdir}/${base_name}_TranscriptsToPeakEdges.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $transcripts_to_edges_out + else + echo No file $outfile >&2 + fi +fi +if [ ! -z "$transcripts_to_edges_summary" ] ; then + outfile=${outdir}/${base_name}_TranscriptsToPeakEdges_summary.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $transcripts_to_edges_summary + else + echo No file $outfile >&2 + fi +fi +# +# TSS to Peak Edges +if [ ! -z "$tss_to_edges_out" ] ; then + outfile=${outdir}/${base_name}_TSSToPeakEdges.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $tss_to_edges_out + else + echo No file $outfile >&2 + fi +fi +if [ ! -z "$tss_to_edges_summary" ] ; then + outfile=${outdir}/${base_name}_TSSToPeakEdges_summary.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $tss_to_edges_summary + else + echo No file $outfile >&2 + fi +fi +# +# Clean up +/bin/rm -rf $outdir +# +# Done |
| b |
| diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_wrapper.xml Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,262 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@-0">\n+ <description>Integrated analysis of gene expression data and ChIP data</description>\n+ <macros>\n+ <import>rnachipintegrator_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+ <command interpreter="bash">rnachipintegrator_wrapper.sh\n+ #if str( $analysis_options.peak_type ) == "summits"\n+ #if str( $analysis_options.window ) != ""\n+ --window=$analysis_options.window\n+ #end if\n+ #if str( $analysis_options.cutoff ) != ""\n+ --cutoff=$analysis_options.cutoff\n+ #end if\n+ #end if\n+ #if str( $analysis_options.peak_type ) == "regions"\n+ #if str( $analysis_options.edge_cutoff ) != ""\n+ --edge-cutoff=$analysis_options.edge_cutoff\n+ #end if\n+ #if str( $analysis_options.number ) != ""\n+ --number=$analysis_options.number\n+ #end if\n+ #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end ))\n+ --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end\n+ #end if\n+ #if $analysis_options.pad_output\n+ --pad\n+ #end if\n+ #end if\n+ $rnaseq $chipseq\n+ --output_xls $xls_output\n+ #if $results_as_zip\n+ --zip_file $zip_file\n+ #else\n+ #if str( $analysis_options.peak_type ) == "summits"\n+ --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out\n+ #end if\n+ #if str( $analysis_options.peak_type ) == "regions"\n+ --peak_outputs $transcripts_to_edges_out\n+ $transcripts_to_edges_summary\n+ $tss_to_edges_out\n+ $tss_to_edges_summary\n+ #end if\n+ #end if\n+ </command>\n+ <inputs>\n+ <param format="tabular" name="rnaseq" type="data" label="Gene expression data file" />\n+ <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" />\n+ <conditional name="analysis_options">\n+ <!-- user must specify if ChIP peaks are summits or regions -->\n+ <param name="peak_type" type="select" label="ChIP peaks are"\n+\t help="Options and outputs depend on whether ChIP data are summits or regions">\n+ <option value="summits">summits</option>\n+ <option value="regions">regions</option>\n+ </param>\n+ <when value="summits">\n+ <param name="window" type="integer" value="20000" optional="true"\n+\t label="Maximum distance a peak can be from each transcript\n+\t\t TSS before being omitted from analysis" />\n+ <param name="cutoff" type="integer" value="130000" optional="true"\n+\t label="Maximum distance a transcript TSS can be from each\n+\t\t peak before being omitted from the analysis" />\n+ </when>\n+ <when value="regions">\n+ <param name="edge_cutoff" type="integer" value="10000" optional="true"\n+\t label="Maximum distance a transcript edge can be from the\n+\t\t peak edge before being omitted from the analysis"\n+\t help="Set to zero to indicate that no cut off should be applied" />\n+ <param name="number" type="integer" value="4" optional="true"\n+\t label="Maximum number of transcripts per peak to report from\n+\t\t from the analysis" />\n+ <param name="promoter_start" type="integer" value="-10000" optional="true"\n+\t label="Start of promoter region with respect to gene TSS" />\n+ <param name="promoter_end" type="integer" value="2500" optional="true"\n+\t label="End of promoter region with respect to gene TSS" />\n+ <param name="pad_output" type="boolean" checked="false" truevalue="yes"\n+\t label="Output same number of lines for each peak"\n+\t help="Add blank lines in output for peaks with fewer than maximum number\n+\t\t of hits (--pad)" />\n+ </when>\n+ </conditional>\n+ <param name="results_as_zip" type="boolean" checked="false" truevalue="yes"\n+ label="Put output tab-delimited files into a single zip archive" />\n+ </inputs>\n+ <outputs>\n+ <!-- Always produce XLS out'..b'peaks to each transcript\n+and vice versa.\n+\n+For ChIP peaks defined as regions the following analyses are performed:\n+\n+ * **TranscriptsToPeakEdges**: reports the nearest transcripts with the smallest\n+ distance from either their TSS or TES to the nearest peak edge.\n+\n+ * **TSSToPeakEdges**: reports the nearest transcripts with the smallest distance\n+ from their TSS to the nearest peak edge.\n+\n+For ChIP peaks defined as summits:\n+\n+ * **TSSToSummits**: reports the nearest transcripts with the smallest distance\n+ from the TSS to the nearest peak summit.\n+\n+ * **PeaksToTranscripts**: reports the nearest peak summits with the smallest\n+ distance to either the TSS or TES of each transcript.\n+\n+The program was originally written specifically for ChIP-Seq and RNA-Seq data\n+but works equally well for ChIP-chip and microarray expression data, and can\n+also be used to integrate any set of genomic features (e.g. canonical genes,\n+CpG islands) with expression data.\n+\n+RnaChipIntgerator can be obtained from\n+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+The expression data must be in a tab-delimited file with the following columns\n+of data for each genomic feature (one feature per line):\n+\n+====== ========== ======================================================================\n+Column Name Description\n+====== ========== ======================================================================\n+ 1 ID Name used to identify the feature in the output\n+ 2 chr Chromosome name\n+ 3 start Start position of the feature\n+ 4 end End position of the feature\n+ 5 strand Must be either \'+\' or \'-\'\n+ 6 diff_expr Optional: indicates feature is differentially expressed (1) or not (0)\n+====== ========== ======================================================================\n+\n+The ChIP-seq data must be in a tab-delimited file with 3 columns of data for each\n+ChIP peak (one per line):\n+\n+====== ========== ======================================================================\n+Column Name Description\n+====== ========== ======================================================================\n+ 1 chr Chromosome name (must match one of those in expression data file)\n+ 2 start Start position of the peak \n+ 3 end End position of the peak (start + 1 for summit data)\n+====== ========== ======================================================================\n+\n+The ChIP peak data can be either the summit (in which case \'end\' - \'start\' = 1) or the\n+entire extent of the binding region (with \'start\' and \'end\' indicating the limits).\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+The outputs from this tool vary depending on the type of data that is input, however\n+generally there is one tab-delimited results file for each analysis described above\n+in the **What it does** section (some analyses output a second file with just the\n+"best" hits).\n+\n+A history item will be generated for each output file, unless the option to put them\n+into a single zip archive is selected; this archive file will have to be downloaded\n+and unzipped on your local machine. It is recommended that you refer to the\n+RnaChipIntegrator documentation for information on the contents of each output file:\n+https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown\n+\n+In addition an Excel spreadsheet (with one page for each analysis performed) is always\n+produced.\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Credits**\n+\n+This Galaxy tool has been developed within the Bioinformatics Core Facility at the\n+University of Manchester. It runs the RnaChipIntegrator package which has also been\n+developed by this group, and is documented at\n+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/\n+\n+Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/ChIP_peaks.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ChIP_peaks.txt Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,70 @@ +#peak s e +chr1 10617233 10617437 +chr1 108747519 108747791 +chr1 120760212 120760461 +chr1 132950929 132951247 +chr1 133114860 133115015 +chr1 135582677 135582828 +chr1 135851853 135852218 +chr1 136956468 136956598 +chr1 13829227 13829564 +chr1 138437726 138437860 +chr1 140381656 140381785 +chr1 145591041 145591176 +chr1 154971572 154971673 +chr1 155123313 155123435 +chr1 158510523 158510813 +chr1 158537267 158537411 +chr1 158580638 158580759 +chr1 158835251 158835391 +chr1 159240736 159240866 +chr1 163827897 163828062 +chr1 164215623 164215935 +chr1 167222964 167223261 +chr1 167906284 167906554 +chr1 170255081 170255260 +chr1 17030405 17030545 +chr1 172620779 172620912 +chr1 172620917 172621080 +chr1 174376470 174376659 +chr1 181061299 181061446 +chr1 182479646 182479905 +chr1 185854947 185855105 +chr1 194258648 194259032 +chr1 194645118 194645475 +chr1 194957396 194957723 +chr1 195324443 195324741 +chr1 195330701 195330930 +chr1 195338316 195338616 +chr1 195342728 195342985 +chr1 195384767 195385195 +chr1 197057796 197057843 +chr1 24609562 24609623 +chr1 24609923 24609992 +chr1 24730996 24731077 +chr1 26734195 26734485 +chr1 34206924 34207100 +chr1 36106813 36107058 +chr1 39492140 39492513 +chr1 40325917 40326123 +chr1 44195449 44195639 +chr1 52625416 52625560 +chr1 54631692 54631815 +chr1 55283572 55283675 +chr1 63664888 63665018 +chr1 72769824 72770056 +chr1 72770058 72770226 +chr1 72815517 72815742 +chr1 75481920 75482054 +chr1 77457642 77457791 +chr1 78630893 78631160 +chr1 88408969 88409267 +chr1 89989553 89989714 +chr1 90412932 90413132 +chr1 90592499 90592629 +chr1 91496003 91496145 +chr1 91496155 91496319 +chr1 92070253 92070431 +chr1 95186508 95186637 +chr1 9619046 9619167 +chr1 9619175 9619382 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/ChIP_summits.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ChIP_summits.txt Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,654 @@\n+#peak\tmid\tplus1\r\n+chr10\t106033584\t106033585\r\n+chr10\t106033751\t106033752\r\n+chr10\t107429926\t107429927\r\n+chr10\t114752719\t114752720\r\n+chr10\t114994096\t114994097\r\n+chr10\t127058840\t127058841\r\n+chr10\t127184557\t127184558\r\n+chr10\t13089536\t13089537\r\n+chr10\t13408622\t13408623\r\n+chr10\t17725474\t17725475\r\n+chr10\t21862583\t21862584\r\n+chr10\t21862774\t21862775\r\n+chr10\t31587625\t31587626\r\n+chr10\t41613298\t41613299\r\n+chr10\t43640892\t43640893\r\n+chr10\t43740181\t43740182\r\n+chr10\t45093322\t45093323\r\n+chr10\t57702300\t57702301\r\n+chr10\t59362596\t59362597\r\n+chr10\t59693654\t59693655\r\n+chr10\t60613588\t60613589\r\n+chr10\t60696228\t60696229\r\n+chr10\t67567003\t67567004\r\n+chr10\t76664902\t76664903\r\n+chr10\t7707698\t7707699\r\n+chr10\t79808095\t79808096\r\n+chr10\t80126390\t80126391\r\n+chr10\t81033719\t81033720\r\n+chr10\t82306942\t82306943\r\n+chr10\t82517145\t82517146\r\n+chr10\t84922053\t84922054\r\n+chr10\t88433836\t88433837\r\n+chr10\t89195191\t89195192\r\n+chr10\t93642365\t93642366\r\n+chr10\t94183365\t94183366\r\n+chr10\t94306306\t94306307\r\n+chr1\t10627335\t10627336\r\n+chr1\t108757655\t108757656\r\n+chr11\t100148455\t100148456\r\n+chr11\t100964551\t100964552\r\n+chr11\t102973374\t102973375\r\n+chr11\t103196320\t103196321\r\n+chr11\t107278688\t107278689\r\n+chr11\t110241161\t110241162\r\n+chr11\t114563829\t114563830\r\n+chr11\t115639021\t115639022\r\n+chr11\t115836265\t115836266\r\n+chr11\t119827740\t119827741\r\n+chr11\t120952392\t120952393\r\n+chr11\t121341339\t121341340\r\n+chr11\t16560450\t16560451\r\n+chr11\t18798190\t18798191\r\n+chr11\t19003164\t19003165\r\n+chr11\t20247624\t20247625\r\n+chr1\t120770337\t120770338\r\n+chr11\t21483462\t21483463\r\n+chr11\t29514477\t29514478\r\n+chr11\t3000481\t3000482\r\n+chr11\t3266659\t3266660\r\n+chr1\t132961088\t132961089\r\n+chr1\t133124938\t133124939\r\n+chr11\t34495361\t34495362\r\n+chr1\t135592753\t135592754\r\n+chr1\t135862036\t135862037\r\n+chr1\t136966533\t136966534\r\n+chr1\t13839396\t13839397\r\n+chr1\t138447793\t138447794\r\n+chr1\t140391721\t140391722\r\n+chr11\t4116866\t4116867\r\n+chr1\t145601109\t145601110\r\n+chr11\t50300699\t50300700\r\n+chr11\t5481053\t5481054\r\n+chr1\t154981623\t154981624\r\n+chr1\t155133374\t155133375\r\n+chr1\t158520668\t158520669\r\n+chr1\t158547339\t158547340\r\n+chr1\t158590699\t158590700\r\n+chr1\t158845321\t158845322\r\n+chr1\t159250801\t159250802\r\n+chr11\t59272503\t59272504\r\n+chr11\t6069204\t6069205\r\n+chr1\t163837980\t163837981\r\n+chr1\t164225779\t164225780\r\n+chr1\t167233113\t167233114\r\n+chr1\t167916419\t167916420\r\n+chr11\t69572437\t69572438\r\n+chr1\t170265171\t170265172\r\n+chr11\t70397406\t70397407\r\n+chr1\t17040475\t17040476\r\n+chr1\t172630846\t172630847\r\n+chr1\t172630999\t172631000\r\n+chr1\t174386565\t174386566\r\n+chr11\t76126479\t76126480\r\n+chr1\t181071373\t181071374\r\n+chr1\t182489776\t182489777\r\n+chr11\t83860977\t83860978\r\n+chr11\t84381942\t84381943\r\n+chr11\t8483612\t8483613\r\n+chr11\t8541945\t8541946\r\n+chr1\t185865026\t185865027\r\n+chr11\t87257043\t87257044\r\n+chr11\t87967409\t87967410\r\n+chr11\t87967599\t87967600\r\n+chr11\t93986729\t93986730\r\n+chr1\t194268840\t194268841\r\n+chr1\t194655297\t194655298\r\n+chr1\t194967560\t194967561\r\n+chr1\t195334592\t195334593\r\n+chr1\t195340816\t195340817\r\n+chr1\t195348466\t195348467\r\n+chr1\t195352857\t195352858\r\n+chr1\t195394981\t195394982\r\n+chr1\t197067820\t197067821\r\n+chr11\t97171690\t97171691\r\n+chr11\t97233548\t97233549\r\n+chr11\t97297212\t97297213\r\n+chr12\t104299157\t104299158\r\n+chr12\t106237696\t106237697\r\n+chr12\t106674392\t106674393\r\n+chr12\t112330425\t112330426\r\n+chr12\t112477144\t112477145\r\n+chr12\t112975712\t112975713\r\n+chr12\t113981451\t113981452\r\n+chr12\t114119343\t114119344\r\n+chr12\t117853390\t117853391\r\n+chr12\t25562241\t25562242\r\n+chr12\t25648378\t25648379\r\n+chr12\t37211753\t37211754\r\n+chr1\t24619593\t24619594\r\n+chr1\t24619958\t24619959\r\n+chr1\t24741037\t24741038\r\n+chr12\t57923295\t57923296\r\n+chr12\t58725309\t58725310\r\n+chr1\t26744340\t26744341\r\n+chr12\t70755181\t70755182\r\n+chr12\t72971895\t72971896\r\n+chr12\t80608252\t80608253\r\n+chr12\t86926811\t86926812\r\n+chr12\t92932316\t92932317\r\n+chr12\t92984595\t92984596\r\n+chr13\t10082361\t10082362\r\n+chr13\t102618599\t102618600\r\n+chr13\t103679464\t103679465\r\n+chr13\t104768206\t104768207\r\n+chr13\t110051416\t110051417\r\n+chr13\t113548696\t113548697\r\n+chr13\t120276594\t120276595\r\n+chr13\t12578010\t12578011\r\n+chr13\t23610160\t23610161\r\n+chr13\t'..b'31\t72564132\r\n+chr5\t73646186\t73646187\r\n+chr5\t87159785\t87159786\r\n+chr5\t90818821\t90818822\r\n+chr5\t99781594\t99781595\r\n+chr6\t100518848\t100518849\r\n+chr6\t103599133\t103599134\r\n+chr6\t113116711\t113116712\r\n+chr6\t121080230\t121080231\r\n+chr6\t127325975\t127325976\r\n+chr6\t127381753\t127381754\r\n+chr6\t127425244\t127425245\r\n+chr6\t128054836\t128054837\r\n+chr6\t128289233\t128289234\r\n+chr6\t128326644\t128326645\r\n+chr6\t128547343\t128547344\r\n+chr6\t134445175\t134445176\r\n+chr6\t134445312\t134445313\r\n+chr6\t143811364\t143811365\r\n+chr6\t146887669\t146887670\r\n+chr6\t147297840\t147297841\r\n+chr6\t17267124\t17267125\r\n+chr6\t33926636\t33926637\r\n+chr6\t37242315\t37242316\r\n+chr6\t47601314\t47601315\r\n+chr6\t49172166\t49172167\r\n+chr6\t51351355\t51351356\r\n+chr6\t56806957\t56806958\r\n+chr6\t67253361\t67253362\r\n+chr6\t76927942\t76927943\r\n+chr6\t83071812\t83071813\r\n+chr6\t83093011\t83093012\r\n+chr6\t86130730\t86130731\r\n+chr6\t87137073\t87137074\r\n+chr6\t87222111\t87222112\r\n+chr6\t94625281\t94625282\r\n+chr7\t104849801\t104849802\r\n+chr7\t117975070\t117975071\r\n+chr7\t119647132\t119647133\r\n+chr7\t119813749\t119813750\r\n+chr7\t120393123\t120393124\r\n+chr7\t120874367\t120874368\r\n+chr7\t123336714\t123336715\r\n+chr7\t125720143\t125720144\r\n+chr7\t126039427\t126039428\r\n+chr7\t127004913\t127004914\r\n+chr7\t128854935\t128854936\r\n+chr7\t128984541\t128984542\r\n+chr7\t134819118\t134819119\r\n+chr7\t135696903\t135696904\r\n+chr7\t137484210\t137484211\r\n+chr7\t137768001\t137768002\r\n+chr7\t138009297\t138009298\r\n+chr7\t138123566\t138123567\r\n+chr7\t138123699\t138123700\r\n+chr7\t139426142\t139426143\r\n+chr7\t146041529\t146041530\r\n+chr7\t147156352\t147156353\r\n+chr7\t148379180\t148379181\r\n+chr7\t148379362\t148379363\r\n+chr7\t148629281\t148629282\r\n+chr7\t150571560\t150571561\r\n+chr7\t152450338\t152450339\r\n+chr7\t152450519\t152450520\r\n+chr7\t16562058\t16562059\r\n+chr7\t16894872\t16894873\r\n+chr7\t17429367\t17429368\r\n+chr7\t20044401\t20044402\r\n+chr7\t26061110\t26061111\r\n+chr7\t26574315\t26574316\r\n+chr7\t28010205\t28010206\r\n+chr7\t30227710\t30227711\r\n+chr7\t30256558\t30256559\r\n+chr7\t35861923\t35861924\r\n+chr7\t56809068\t56809069\r\n+chr7\t87336398\t87336399\r\n+chr7\t88092779\t88092780\r\n+chr7\t89920499\t89920500\r\n+chr8\t10576464\t10576465\r\n+chr8\t107426996\t107426997\r\n+chr8\t109087961\t109087962\r\n+chr8\t109275046\t109275047\r\n+chr8\t109334564\t109334565\r\n+chr8\t113806188\t113806189\r\n+chr8\t119851483\t119851484\r\n+chr8\t121354388\t121354389\r\n+chr8\t129127362\t129127363\r\n+chr8\t129549456\t129549457\r\n+chr8\t13548998\t13548999\r\n+chr8\t13668465\t13668466\r\n+chr8\t14306960\t14306961\r\n+chr8\t17594804\t17594805\r\n+chr8\t19919526\t19919527\r\n+chr8\t19924810\t19924811\r\n+chr8\t22870138\t22870139\r\n+chr8\t23921280\t23921281\r\n+chr8\t24206095\t24206096\r\n+chr8\t34068894\t34068895\r\n+chr8\t37107644\t37107645\r\n+chr8\t4586605\t4586606\r\n+chr8\t70850825\t70850826\r\n+chr8\t71717281\t71717282\r\n+chr8\t73173598\t73173599\r\n+chr8\t73183558\t73183559\r\n+chr8\t73297497\t73297498\r\n+chr8\t81256455\t81256456\r\n+chr8\t86143616\t86143617\r\n+chr8\t87180694\t87180695\r\n+chr8\t88126748\t88126749\r\n+chr8\t93828640\t93828641\r\n+chr8\t97699878\t97699879\r\n+chr9\t100543647\t100543648\r\n+chr9\t103988283\t103988284\r\n+chr9\t106273656\t106273657\r\n+chr9\t107478162\t107478163\r\n+chr9\t108851463\t108851464\r\n+chr9\t110183808\t110183809\r\n+chr9\t111053664\t111053665\r\n+chr9\t116828689\t116828690\r\n+chr9\t118884586\t118884587\r\n+chr9\t120883928\t120883929\r\n+chr9\t123371104\t123371105\r\n+chr9\t13408238\t13408239\r\n+chr9\t14466849\t14466850\r\n+chr9\t14480293\t14480294\r\n+chr9\t24346538\t24346539\r\n+chr9\t3258857\t3258858\r\n+chr9\t42777363\t42777364\r\n+chr9\t43528251\t43528252\r\n+chr9\t43585984\t43585985\r\n+chr9\t44215148\t44215149\r\n+chr9\t44307103\t44307104\r\n+chr9\t54460731\t54460732\r\n+chr9\t66728918\t66728919\r\n+chr9\t66794084\t66794085\r\n+chr9\t67556540\t67556541\r\n+chr9\t70477636\t70477637\r\n+chr9\t72497695\t72497696\r\n+chr9\t72916030\t72916031\r\n+chr9\t74815214\t74815215\r\n+chr9\t75371664\t75371665\r\n+chr9\t8033087\t8033088\r\n+chr9\t8055015\t8055016\r\n+chr9\t83462792\t83462793\r\n+chr9\t86714892\t86714893\r\n+chrX\t109484691\t109484692\r\n+chrX\t137172820\t137172821\r\n+chrX\t139917606\t139917607\r\n+chrX\t140401017\t140401018\r\n+chrX\t163589625\t163589626\r\n+chrX\t166360754\t166360755\r\n+chrX\t166427362\t166427363\r\n+chrX\t166432950\t166432951\r\n+chrX\t84483714\t84483715\r\n+chrX\t98516735\t98516736\r\n' |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/ExpressionData.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ExpressionData.txt Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,957 @@\n+#RefSeq_Gene Symbol\tchr1\tstart\tstop\tstrand\tdiff_exp\r\n+AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t1\r\n+AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t1\r\n+AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t1\r\n+AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t1\r\n+AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t1\r\n+BC006931_AI597479\tchr1\t43153807\t43172843\t+\t1\r\n+BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t1\r\n+BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t1\r\n+BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t1\r\n+BC031781_BC031781\tchr1\t182781250\t182798240\t+\t1\r\n+BC034187_BC035947\tchr1\t78493611\t78497758\t-\t1\r\n+BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t1\r\n+BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\t1\r\n+BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t1\r\n+BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t1\r\n+BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t1\r\n+BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t1\r\n+BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t1\r\n+BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t1\r\n+BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t1\r\n+BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\t1\r\n+BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\t1\r\n+BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t1\r\n+BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t1\r\n+BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t1\r\n+BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t1\r\n+BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t1\r\n+BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t1\r\n+BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t1\r\n+BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t0\r\n+BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t0\r\n+BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\t0\r\n+BC089561_Cep350\tchr1\t157692096\t157820375\t-\t0\r\n+BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t0\r\n+BC147657_9630028B13Rik\tchr1\t187253234\t187265698\t-\t0\r\n+ENSMUST00000027997_Rgs5\tchr1\t171625108\t171625913\t+\t0\r\n+ENSMUST00000051203_1700001G17Rik\tchr1\t33726669\t33727551\t+\t0\r\n+ENSMUST00000054333_A130050O07Rik\tchr1\t139823828\t139826840\t+\t0\r\n+ENSMUST00000056879_C230029F24Rik\tchr1\t49301475\t49397265\t+\t0\r\n+ENSMUST00000057543_A730013G03Rik\tchr1\t194659323\t194661397\t-\t0\r\n+ENSMUST00000062637_4930470H14Rik\tchr1\t175156866\t175201240\t+\t0\r\n+ENSMUST00000070048_ENSMUSG00000056128\tchr1\t92571736\t92576368\t+\t0\r\n+ENSMUST00000070987_EG433384\tchr1\t183781705\t183783320\t-\t0\r\n+ENSMUST00000072395_Olfr1406\tchr1\t175113651\t175120746\t-\t0\r\n+ENSMUST00000094288_Wdr64\tchr1\t177654798\t177798070\t+\t0\r\n+ENSMUST00000094950_Pgap1\tchr1\t54529849\t54614539\t-\t0\r\n+ENSMUST00000097776_Cnnm3\tchr1\t36567938\t36585164\t+\t0\r\n+EU429481_Igfn1\tchr1\t137825893\t137890307\t-\t0\r\n+FJ024495_Ildr2\tchr1\t168236882\t168239692\t-\t0\r\n+FJ210934_Unc80\tchr1\t66514856\t66556109\t+\t0\r\n+NM_001001565_Chpf\tchr1\t75470923\t75476437\t-\t0\r\n+NM_001001809_Olfr218\tchr1\t175130421\t175134469\t+\t0\r\n+NM_001001883_Hecw2\tchr1\t53867026\t54252002\t-\t0\r\n+NM_001003917_Atg9a\tchr1\t75177439\t75189181\t-\t0\r\n+NM_001004173_Sgpp2\tchr1\t78306692\t78416864\t+\t0\r\n+NM_001005423_Mreg\tchr1\t72170192\t72258895\t-\t0\r\n+NM_001005507_Smg7\tchr1\t154684125\t154750410\t-\t0\r\n+NM_001005508_Arhgap30\tchr1\t173319072\t173340822\t+\t0\r\n+NM_001005520_Olfr244\tchr1\t176032571\t176067605\t-\t0\r\n+NM_001008419_Aox3l1\tchr1\t58335180\t58437083\t+\t0\r\n+NM_001008426_EG433365\tchr1\t155721475\t155724001\t+\t0\r\n+NM_001008533_Adora1\tchr1\t136095799\t136181661\t-\t0\r\n+NM_001009940_Il19\tchr1\t132786042\t132915234\t-\t0\r\n+NM_001011525_Olfr1415\tchr1\t94376258\t94381054\t-\t0\r\n+NM_001011525_Olfr1415\tchr1\t94407669\t94418761\t-\t0\r\n+NM_001011684_Nms\tchr1\t38995917\t39007113\t+\t0\r\n+NM_001011873_Xkr9\tchr1\t13658862\t13691794\t+\t0\r\n+NM_001011874_Xkr4\tchr1\t3203722\t3713108\t-\t0\r\n+NM_001012330_Zfp238\tchr1\t179359958\t179380892\t+\t0\r\n+NM_001013374_Lman2l\tchr1\t36362897\t36502078\t-\t0\r\n+NM_001013382_Lrrc52\tchr1\t169375806\t169397136\t-\t0\r\n+NM_001013771_Gm973\tchr1\t59573136\t59693241\t+\t0\r\n+NM_001013779_Aim2\tchr1\t175385835\t175396165\t+\t0\r\n+NM_001014974_Ttll4\tchr1\t74708314\t74748400\t+\t0\r\n+NM_001024721_BC094916\tchr1\t175451304\t175466101\t-\t0\r\n+NM_001024945_Qsox1\tchr1\t157625296\t157670499\t-\t0\r\n+NM_001025156_Ccdc93'..b's\tchr1\t130260284\t130314013\t-\t0\r\n+NM_177587_Aqp12\tchr1\t94886487\t94908846\t+\t0\r\n+NM_177604_AA986860\tchr1\t132628563\t132644539\t+\t0\r\n+NM_177643_Zfp281\tchr1\t138487073\t138526617\t+\t0\r\n+NM_177646_Dgkd\tchr1\t89749836\t89841946\t+\t0\r\n+NM_177722_6030422M02Rik\tchr1\t9898713\t9932156\t+\t0\r\n+NM_177723_Vsig8\tchr1\t174486069\t174513273\t+\t0\r\n+NM_177724_D230039L06Rik\tchr1\t180426979\t180686112\t+\t0\r\n+NM_177756_Glt25d2\tchr1\t154223175\t154357825\t+\t0\r\n+NM_177757_Kif26b\tchr1\t180720593\t180862983\t+\t0\r\n+NM_177781_Trpa1\tchr1\t14861962\t14909072\t-\t0\r\n+NM_177834_Cpa6\tchr1\t10314801\t10710026\t-\t0\r\n+NM_177838_Fam163a\tchr1\t157923096\t158135544\t-\t0\r\n+NM_177839_Tnn\tchr1\t161966935\t162084477\t-\t0\r\n+NM_178051_Mterfd2\tchr1\t95195779\t95202630\t-\t0\r\n+NM_178055_Dnajb2\tchr1\t75233016\t75242264\t+\t0\r\n+NM_178119_Agap1\tchr1\t91351421\t91791845\t+\t0\r\n+NM_178241_Il8ra\tchr1\t74238380\t74241205\t-\t0\r\n+NM_178243_5830403L16Rik\tchr1\t155697272\t155747352\t-\t0\r\n+NM_178244_Teddm1\tchr1\t155724147\t155740188\t+\t0\r\n+NM_178399_3110035E14Rik\tchr1\t9591248\t9617222\t+\t0\r\n+NM_178405_Atp1a2\tchr1\t174201852\t174233438\t-\t0\r\n+NM_178593_Rcsd1\tchr1\t167572007\t167639868\t-\t0\r\n+NM_178598_Tagln2\tchr1\t174430123\t174475991\t+\t0\r\n+NM_178601_Imp4\tchr1\t34496377\t34511555\t+\t0\r\n+NM_178632_Ints7\tchr1\t193399085\t193447550\t+\t0\r\n+NM_178653_Sccpdh\tchr1\t181598088\t181617593\t+\t0\r\n+NM_178690_Rab3gap1\tchr1\t129765355\t129840723\t+\t0\r\n+NM_178691_Yod1\tchr1\t132612680\t132618643\t+\t0\r\n+NM_178692_C130074G19Rik\tchr1\t186695805\t186707077\t-\t0\r\n+NM_178775_Rps6kc1\tchr1\t192524091\t192736016\t-\t0\r\n+NM_178779_Rnf152\tchr1\t107176426\t107253513\t-\t0\r\n+NM_178874_Tmcc2\tchr1\t134252895\t134288369\t-\t0\r\n+NM_178883_Gorab\tchr1\t165315039\t165340946\t-\t0\r\n+NM_178884_Obsl1\tchr1\t75482401\t75503218\t-\t0\r\n+NM_181405_Rnpepl1\tchr1\t94807467\t94817954\t+\t0\r\n+NM_181546_Syt14\tchr1\t194713536\t194861959\t-\t0\r\n+NM_181750_R3hdm1\tchr1\t129999892\t130134312\t+\t0\r\n+NM_181796_Gstp2\tchr1\t193897651\t193905509\t-\t0\r\n+NM_182716_Nfasc\tchr1\t134445291\t134638354\t-\t0\r\n+NM_182930_Plekha6\tchr1\t135077806\t135200008\t+\t0\r\n+NM_183019_Arhgef4\tchr1\t34788954\t34873560\t+\t0\r\n+NM_183022_Accn4\tchr1\t75447063\t75470207\t+\t0\r\n+NM_183027_Ap1s3\tchr1\t79591820\t79668545\t-\t0\r\n+NM_183028_Pcmtd1\tchr1\t7079053\t7163709\t+\t0\r\n+NM_183124_Defb41\tchr1\t18241071\t18350659\t-\t0\r\n+NM_183355_Pbx1\tchr1\t170049495\t170512777\t-\t0\r\n+NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t0\r\n+NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t0\r\n+NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t0\r\n+NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t0\r\n+NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t0\r\n+NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t0\r\n+NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\t0\r\n+NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t0\r\n+NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t0\r\n+NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t0\r\n+NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t0\r\n+NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t0\r\n+NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t0\r\n+NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\t0\r\n+NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t0\r\n+NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t0\r\n+NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t0\r\n+NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t0\r\n+NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\t0\r\n+NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t0\r\n+NM_207031_Ano7\tchr1\t95270385\t95302271\t+\t0\r\n+NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t0\r\n+NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t0\r\n+NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t0\r\n+NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t0\r\n+NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t0\r\n+NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t0\r\n+NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t0\r\n+NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t0\r\n+NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t0\r\n+NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t0\r\n+NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\t0\r\n+NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t0\r\n+NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t0\r\n+NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\t0\r\n+NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t0\r\n+NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t0\r\n' |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_canonical_genes.data_manager_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_canonical_genes.data_manager_json Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +{"data_tables": {"rnachipintegrator_canonical_genes": {"value": "dataset_62.dat", "name": "Mouse (mm9)", "dbkey": "mm9"}}} |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_canonical_genes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_canonical_genes.tsv Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,10 @@ +mm9.kgXref.geneSymbol #mm9.knownCanonical.chrom mm9.knownCanonical.chromStart mm9.knownCanonical.chromEnd mm9.knownGene.strand mm9.knownCanonical.transcript mm9.kgXref.refseq +Xkr4 chr1 3204562 3661579 - uc007aeu.1 NM_001011874 +AK149000 chr1 3638391 3648985 - uc007aev.1 +Rp1 chr1 4333587 4350395 - uc007aex.2 NM_011283 +Sox17 chr1 4481008 4486494 - uc007aez.1 NM_011441 +Mrpl15 chr1 4763278 4775807 - uc007aff.2 NM_001177658 +Lypla1 chr1 4797973 4836816 + uc007afh.1 NM_008866 +Tcea1 chr1 4847774 4887990 + uc007afi.2 NM_011541 +Rgs20 chr1 4899656 5060366 - uc007afl.2 NM_001177795 +Atp6v1h chr1 5073253 5152630 + uc007afn.1 NM_133826 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_peaks.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks.txt Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,500 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|
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_peaks.xls |
| b |
| Binary file test-data/mm9_peaks.xls has changed |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_summits.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_summits.txt Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,500 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1094949\n+chr1\t121167893\t121167894\n+chr1\t121340746\t121340747\n+chr1\t121587267\t121587268\n+chr1\t121681260\t121681261\n+chr1\t121816202\t121816203\n+chr1\t123026661\t123026662\n+chr1\t123170986\t123170987\n+chr1\t123685384\t123685385\n+chr1\t123835178\t123835179\n+chr1\t123920817\t123920818\n+chr1\t123949970\t123949971\n+chr1\t124461424\t124461425\n+chr1\t125400371\t125400372\n+chr1\t126171930\t126171931\n+chr1\t126179030\t126179031\n+chr1\t126687579\t126687580\n+chr1\t126712327\t126712328\n+chr1\t126783497\t126783498\n+chr1\t126787012\t126787013\n+chr1\t126963082\t126963083\n+chr1\t127190153\t127190154\n+chr1\t127228396\t127228397\n+chr1\t127507342\t127507343\n+chr1\t127703188\t127703189\n+chr1\t127735504\t127735505\n+chr1\t128049231\t128049232\n+chr1\t128388917\t128388918\n+chr1\t128791747\t128791748\n+chr1\t129571914\t129571915\n+chr1\t129582844\t129582845\n+chr1\t130923911\t130923912\n+chr1\t131245002\t131245003\n+chr1\t131624212\t131624213\n+chr1\t131653028\t131653029\n+chr1\t131673494\t131673495\n+chr1\t131762457\t131762458\n+chr1\t132812150\t132812151\n+chr1\t133122490\t133122491\n+chr1\t133337646\t133337647\n+chr1\t134107973\t134107974\n+chr1\t134516117\t134516118\n+chr1\t134650852\t134650853\n+chr1\t135304596\t135304597\n+chr1\t135346221\t135346222\n+chr1\t135595351\t135595352\n+chr1\t135645557\t135645558\n+chr1\t135794196\t135794197\n+chr1\t135833373\t135833374\n+chr1\t136109219\t136109220\n+chr1\t136151385\t136151386\n+chr1\t136219228\t136219229\n+chr1\t136276302\t136276303\n+chr1\t136409892\t136409893\n+chr1\t136846450\t136846451\n+chr1\t137021089\t137021090\n+chr1\t137057829\t137057830\n+chr1\t137256872\t137256873\n+chr1\t137292997\t137292998\n+chr1\t137340715\t137340716\n+chr1\t137563013\t137563014\n+chr1\t138237818\t138237819\n+chr1\t138288739\t138288740\n+chr1\t138701415\t138701416\n+chr1\t138883160\t138883161\n+chr1\t139093105\t139093106\n+chr1\t139286502\t139286503\n+chr1\t139448680\t139448681\n+chr1\t139944056\t139944057\n+chr1\t140207040\t140207041\n+chr1\t141517452\t141517453\n+chr1\t142087663\t142087664\n+chr1\t142561476\t142561477\n+chr1\t142732555\t142732556\n+chr1\t142765329\t142765330\n+chr1\t142811575\t142811576\n+chr1\t142823331\t142823332\n+chr1\t142985887\t142985888\n+chr1\t143071919\t143071920\n+chr1\t143137676\t143137677\n+chr1\t143684082\t143684083\n+chr1\t143803869\t143803870\n+chr1\t143866547\t143866548\n+chr1\t144585588\t144585589\n+chr1\t145018626\t145018627\n+chr1\t145169340\t145169341\n+chr1\t145286043\t145286044\n+chr1\t145743816\t145743817\n+chr1\t145793073\t145793074\n+chr1\t145943835\t145943836\n+chr1\t145973347\t145973348\n+chr1\t146233793\t146233794\n+chr1\t146349912\t146349913\n+chr1\t146992848\t146992849\n+chr1\t147015972\t147015973\n+chr1\t147919367\t147919368\n+chr1\t148073000\t148073001\n+chr1\t148184896\t148184897\n+chr1\t148571263\t148571264\n+chr1\t148727077\t148727078\n+chr1\t148900032\t148900033\n+chr1\t148988309\t148988310\n+chr1\t149151516\t149151517\n+chr1\t149373423\t149373424\n+chr1\t149547172\t149547173\n+chr1\t149930099\t149930100\n+chr1\t150523771\t150523772\n+chr1\t151852781\t151852782\n+chr1\t151941991\t151941992\n+chr1\t152055844\t152055845\n+chr1\t152768992\t152768993\n+chr1\t153117376\t153117377\n+chr1\t153562593\t153562594\n+chr1\t153617551\t153617552\n+chr1\t154259255\t154259256\n+chr1\t154305193\t154305194\n+chr1\t154793310\t154793311\n+chr1\t154959021\t154959022\n+chr1\t155608292\t155608293\n+chr1\t155676641\t155676642\n+chr1\t155882149\t155882150\n+chr1\t156957961\t156957962\n+chr1\t157054389\t157054390\n+chr1\t157229460\t157229461\n+chr1\t157232537\t157232538\n+chr1\t157353367\t157353368\n+chr1\t157530064\t157530065\n+chr1\t157616665\t157616666\n+chr1\t157708175\t157708176\n+chr1\t157854160\t157854161\n+chr1\t157916567\t157916568\n+chr1\t157960555\t157960556\n+chr1\t158166030\t158166031\n+chr1\t158365460\t158365461\n+chr1\t158890212\t158890213\n+chr1\t159139993\t159139994\n+chr1\t159875548\t159875549\n' |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_summits.xls |
| b |
| Binary file test-data/mm9_summits.xls has changed |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_summits_to_transcripts.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_summits_to_transcripts.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,10 @@ +#geneID chr_RNA start end strand differentially_expressed number_of_peaks chr_ChIP_1 summit_1 distance_1 +Xkr4 chr1 3204562 3661579 - None 1 chr1 3621547 40032 +AK149000 chr1 3638391 3648985 - None 1 chr1 3621547 27438 +Rp1 chr1 4333587 4350395 - None 0 --- --- --- +Sox17 chr1 4481008 4486494 - None 0 --- --- --- +Mrpl15 chr1 4763278 4775807 - None 0 --- --- --- +Lypla1 chr1 4797973 4836816 + None 0 --- --- --- +Tcea1 chr1 4847774 4887990 + None 0 --- --- --- +Rgs20 chr1 4899656 5060366 - None 0 --- --- --- +Atp6v1h chr1 5073253 5152630 + None 0 --- --- --- |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_transcripts_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_transcripts_to_edges.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3213477 3213513 Xkr4 - 3661579 3204562 8915 448066 8915 1 0 +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 +chr1 3621547 3621583 Xkr4 - 3661579 3204562 39996 39996 416985 1 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_transcripts_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_transcripts_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3213477 3213513 Xkr4 - 3661579 3204562 8915 448066 8915 1 0 +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_tss_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_tss_to_edges.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 +chr1 3621547 3621583 Xkr4 - 3661579 3204562 39996 39996 416985 1 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_tss_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_tss_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/mm9_tss_to_summits.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_tss_to_summits.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,504 @@\n+#chr\tstart\tgeneID\tnearest\tTSS\tdistance_to_TSS\tdistance_to_TES\tstrand\tin_the_gene\ttranscripts_inbetween\ttranscript_ids_inbetween\n+chr1\t3213477\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t3542857\tAK149000\t1 of 2\t3648985\t106128\t95534\t-\tNO\t0\t\n+chr1\t3542857\tXkr4\t2 of 2\t3661579\t118722\t-338295\t-\tYES\t1\tAK149000\n+chr1\t3560979\tAK149000\t1 of 2\t3648985\t88006\t77412\t-\tNO\t0\t\n+chr1\t3560979\tXkr4\t2 of 2\t3661579\t100600\t-356417\t-\tYES\t1\tAK149000\n+chr1\t3621547\tAK149000\t1 of 2\t3648985\t27438\t16844\t-\tNO\t0\t\n+chr1\t3621547\tXkr4\t2 of 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| diff -r 000000000000 -r d9c1f2133124 test-data/peaks.xls |
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| Binary file test-data/peaks.xls has changed |
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| diff -r 000000000000 -r d9c1f2133124 test-data/peaks_to_transcripts.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_to_transcripts.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,957 @@\n+#geneID\tchr_RNA\tstart\tend\tstrand\tdifferentially_expressed\tnumber_of_peaks\n+AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t1\t0\n+AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t1\t0\n+AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t1\t0\n+AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t1\t0\n+AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t1\t0\n+BC006931_AI597479\tchr1\t43153807\t43172843\t+\t1\t0\n+BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t1\t0\n+BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t1\t0\n+BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t1\t0\n+BC031781_BC031781\tchr1\t182781250\t182798240\t+\t1\t0\n+BC034187_BC035947\tchr1\t78493611\t78497758\t-\t1\t0\n+BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t1\t0\n+BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\t1\t0\n+BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t1\t0\n+BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t1\t0\n+BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t1\t0\n+BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t1\t0\n+BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t1\t0\n+BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t1\t0\n+BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t1\t0\n+BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\t1\t0\n+BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\t1\t0\n+BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t1\t0\n+BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t1\t0\n+BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t1\t0\n+BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t1\t0\n+BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t1\t0\n+BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t1\t0\n+BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t1\t0\n+BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t0\t0\n+BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t0\t0\n+BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\t0\t0\n+BC089561_Cep350\tchr1\t157692096\t157820375\t-\t0\t0\n+BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t0\t0\n+BC147657_9630028B13Rik\tchr1\t187253234\t187265698\t-\t0\t0\n+ENSMUST00000027997_Rgs5\tchr1\t171625108\t171625913\t+\t0\t0\n+ENSMUST00000051203_1700001G17Rik\tchr1\t33726669\t33727551\t+\t0\t0\n+ENSMUST00000054333_A130050O07Rik\tchr1\t139823828\t139826840\t+\t0\t0\n+ENSMUST00000056879_C230029F24Rik\tchr1\t49301475\t49397265\t+\t0\t0\n+ENSMUST00000057543_A730013G03Rik\tchr1\t194659323\t194661397\t-\t0\t0\n+ENSMUST00000062637_4930470H14Rik\tchr1\t175156866\t175201240\t+\t0\t0\n+ENSMUST00000070048_ENSMUSG00000056128\tchr1\t92571736\t92576368\t+\t0\t0\n+ENSMUST00000070987_EG433384\tchr1\t183781705\t183783320\t-\t0\t0\n+ENSMUST00000072395_Olfr1406\tchr1\t175113651\t175120746\t-\t0\t0\n+ENSMUST00000094288_Wdr64\tchr1\t177654798\t177798070\t+\t0\t0\n+ENSMUST00000094950_Pgap1\tchr1\t54529849\t54614539\t-\t0\t0\n+ENSMUST00000097776_Cnnm3\tchr1\t36567938\t36585164\t+\t0\t0\n+EU429481_Igfn1\tchr1\t137825893\t137890307\t-\t0\t0\n+FJ024495_Ildr2\tchr1\t168236882\t168239692\t-\t0\t0\n+FJ210934_Unc80\tchr1\t66514856\t66556109\t+\t0\t0\n+NM_001001565_Chpf\tchr1\t75470923\t75476437\t-\t0\t0\n+NM_001001809_Olfr218\tchr1\t175130421\t175134469\t+\t0\t0\n+NM_001001883_Hecw2\tchr1\t53867026\t54252002\t-\t0\t0\n+NM_001003917_Atg9a\tchr1\t75177439\t75189181\t-\t0\t0\n+NM_001004173_Sgpp2\tchr1\t78306692\t78416864\t+\t0\t0\n+NM_001005423_Mreg\tchr1\t72170192\t72258895\t-\t0\t0\n+NM_001005507_Smg7\tchr1\t154684125\t154750410\t-\t0\t0\n+NM_001005508_Arhgap30\tchr1\t173319072\t173340822\t+\t0\t0\n+NM_001005520_Olfr244\tchr1\t176032571\t176067605\t-\t0\t0\n+NM_001008419_Aox3l1\tchr1\t58335180\t58437083\t+\t0\t0\n+NM_001008426_EG433365\tchr1\t155721475\t155724001\t+\t0\t0\n+NM_001008533_Adora1\tchr1\t136095799\t136181661\t-\t0\t0\n+NM_001009940_Il19\tchr1\t132786042\t132915234\t-\t0\t0\n+NM_001011525_Olfr1415\tchr1\t94376258\t94381054\t-\t0\t0\n+NM_001011525_Olfr1415\tchr1\t94407669\t94418761\t-\t0\t0\n+NM_001011684_Nms\tchr1\t38995917\t39007113\t+\t0\t0\n+NM_001011873_Xkr9\tchr1\t13658862\t13691794\t+\t0\t0\n+NM_001011874_Xkr4\tchr1\t3203722\t3713108\t-\t0\t0\n+NM_001012330_Zfp238\tchr1\t179359958\t179380892\t+\t0\t0\n+NM_001013374_Lman2l\tchr1\t36362897\t36502078\t-\t0\t0\n+NM_001013382_Lrrc52\tchr1\t169375806\t169397136\t-\t0\t0\n+NM_001013771_Gm973\tchr1\t59573136\t59693241\t+\t0\t0\n+NM_001013779_Aim2\tchr1\t175385835\t175396165\t+\t0\t0\n+NM_001014974_Ttll4\tchr1\t74708314\t74748400\t+\t0\t0\n+NM_001024721_BC094916\tchr1\t'..b'77604_AA986860\tchr1\t132628563\t132644539\t+\t0\t0\n+NM_177643_Zfp281\tchr1\t138487073\t138526617\t+\t0\t0\n+NM_177646_Dgkd\tchr1\t89749836\t89841946\t+\t0\t0\n+NM_177722_6030422M02Rik\tchr1\t9898713\t9932156\t+\t0\t0\n+NM_177723_Vsig8\tchr1\t174486069\t174513273\t+\t0\t0\n+NM_177724_D230039L06Rik\tchr1\t180426979\t180686112\t+\t0\t0\n+NM_177756_Glt25d2\tchr1\t154223175\t154357825\t+\t0\t0\n+NM_177757_Kif26b\tchr1\t180720593\t180862983\t+\t0\t0\n+NM_177781_Trpa1\tchr1\t14861962\t14909072\t-\t0\t0\n+NM_177834_Cpa6\tchr1\t10314801\t10710026\t-\t0\t0\n+NM_177838_Fam163a\tchr1\t157923096\t158135544\t-\t0\t0\n+NM_177839_Tnn\tchr1\t161966935\t162084477\t-\t0\t0\n+NM_178051_Mterfd2\tchr1\t95195779\t95202630\t-\t0\t0\n+NM_178055_Dnajb2\tchr1\t75233016\t75242264\t+\t0\t0\n+NM_178119_Agap1\tchr1\t91351421\t91791845\t+\t0\t0\n+NM_178241_Il8ra\tchr1\t74238380\t74241205\t-\t0\t0\n+NM_178243_5830403L16Rik\tchr1\t155697272\t155747352\t-\t0\t0\n+NM_178244_Teddm1\tchr1\t155724147\t155740188\t+\t0\t0\n+NM_178399_3110035E14Rik\tchr1\t9591248\t9617222\t+\t0\t0\n+NM_178405_Atp1a2\tchr1\t174201852\t174233438\t-\t0\t0\n+NM_178593_Rcsd1\tchr1\t167572007\t167639868\t-\t0\t0\n+NM_178598_Tagln2\tchr1\t174430123\t174475991\t+\t0\t0\n+NM_178601_Imp4\tchr1\t34496377\t34511555\t+\t0\t0\n+NM_178632_Ints7\tchr1\t193399085\t193447550\t+\t0\t0\n+NM_178653_Sccpdh\tchr1\t181598088\t181617593\t+\t0\t0\n+NM_178690_Rab3gap1\tchr1\t129765355\t129840723\t+\t0\t0\n+NM_178691_Yod1\tchr1\t132612680\t132618643\t+\t0\t0\n+NM_178692_C130074G19Rik\tchr1\t186695805\t186707077\t-\t0\t0\n+NM_178775_Rps6kc1\tchr1\t192524091\t192736016\t-\t0\t0\n+NM_178779_Rnf152\tchr1\t107176426\t107253513\t-\t0\t0\n+NM_178874_Tmcc2\tchr1\t134252895\t134288369\t-\t0\t0\n+NM_178883_Gorab\tchr1\t165315039\t165340946\t-\t0\t0\n+NM_178884_Obsl1\tchr1\t75482401\t75503218\t-\t0\t0\n+NM_181405_Rnpepl1\tchr1\t94807467\t94817954\t+\t0\t0\n+NM_181546_Syt14\tchr1\t194713536\t194861959\t-\t0\t0\n+NM_181750_R3hdm1\tchr1\t129999892\t130134312\t+\t0\t0\n+NM_181796_Gstp2\tchr1\t193897651\t193905509\t-\t0\t0\n+NM_182716_Nfasc\tchr1\t134445291\t134638354\t-\t0\t0\n+NM_182930_Plekha6\tchr1\t135077806\t135200008\t+\t0\t0\n+NM_183019_Arhgef4\tchr1\t34788954\t34873560\t+\t0\t0\n+NM_183022_Accn4\tchr1\t75447063\t75470207\t+\t0\t0\n+NM_183027_Ap1s3\tchr1\t79591820\t79668545\t-\t0\t0\n+NM_183028_Pcmtd1\tchr1\t7079053\t7163709\t+\t0\t0\n+NM_183124_Defb41\tchr1\t18241071\t18350659\t-\t0\t0\n+NM_183355_Pbx1\tchr1\t170049495\t170512777\t-\t0\t0\n+NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t0\t0\n+NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t0\t0\n+NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t0\t0\n+NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t0\t0\n+NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t0\t0\n+NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t0\t0\n+NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\t0\t0\n+NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t0\t0\n+NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t0\t0\n+NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t0\t0\n+NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t0\t0\n+NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t0\t0\n+NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t0\t0\n+NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\t0\t0\n+NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t0\t0\n+NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t0\t0\n+NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t0\t0\n+NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t0\t0\n+NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\t0\t0\n+NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t0\t0\n+NM_207031_Ano7\tchr1\t95270385\t95302271\t+\t0\t0\n+NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t0\t0\n+NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t0\t0\n+NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t0\t0\n+NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t0\t0\n+NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t0\t0\n+NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t0\t0\n+NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t0\t0\n+NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t0\t0\n+NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t0\t0\n+NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t0\t0\n+NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\t0\t0\n+NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t0\t0\n+NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t0\t0\n+NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\t0\t0\n+NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t0\t0\n+NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t0\t0\n' |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/rnachipintegrator_canonical_genes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnachipintegrator_canonical_genes.loc Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +mm9_test mm9 mm9 ${__HERE__}/mm9_canonical_genes.tsv |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/summits.xls |
| b |
| Binary file test-data/summits.xls has changed |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/transcripts_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_to_edges.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/transcripts_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/tss_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_to_edges.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/tss_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 |
| b |
| diff -r 000000000000 -r d9c1f2133124 test-data/tss_to_summits.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_to_summits.out Tue Jun 30 06:44:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,654 @@\n+#chr\tstart\tgeneID\tnearest\tTSS\tdistance_to_TSS\tdistance_to_TES\tstrand\tin_the_gene\ttranscripts_inbetween\ttranscript_ids_inbetween\n+chr10\t106033584\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t106033751\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t107429926\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t114752719\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t114994096\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t127058840\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t127184557\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t13089536\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t13408622\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t17725474\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t21862583\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t21862774\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t31587625\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t41613298\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t43640892\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t43740181\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t45093322\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t57702300\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t59362596\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t59693654\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t60613588\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t60696228\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t67567003\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t76664902\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t7707698\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t79808095\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t80126390\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t81033719\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t82306942\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t82517145\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t84922053\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t88433836\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t89195191\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t93642365\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t94183365\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr10\t94306306\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t10627335\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t108757655\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t100148455\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t100964551\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t102973374\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t103196320\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t107278688\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t110241161\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t114563829\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t115639021\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t115836265\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t119827740\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t120952392\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t121341339\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t16560450\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t18798190\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t19003164\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t20247624\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t120770337\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t21483462\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t29514477\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t3000481\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t3266659\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t132961088\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t133124938\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t34495361\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t135592753\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t135862036\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t136966533\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t13839396\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t138447793\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t140391721\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t4116866\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t145601109\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t50300699\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t5481053\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t154981623\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t155133374\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158520668\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158547339\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158590699\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158845321\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t159250801\tBC055845_2810025M15Rik\t1 of 1\t159342483\t91682\t99552\t+\tNO\t0\t\n+chr11\t59272503\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t6069204\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t163837980\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t164225779\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t167233113\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t167916419\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t69572437\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t170265171\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t70397406\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t17040475\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t172630846\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t172630999\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t174386565\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t76126479\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t181071373\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t182489776\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t83860977\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t84381942\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t8483612\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t8541945\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t185865026\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t87257043\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t87967409\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t87967599\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr11\t93986729\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t194268840\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t194655297\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t194967560\tBC055955_A130010J15Rik\t1 of 1\t194999663\t32103\t36455\t+\tNO\t1\tNM_016851_Irf6\n+chr1\t195334592\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t195340816\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t195348466\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t'..b'1\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t104849801\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t117975070\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t119647132\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t119813749\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t120393123\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t120874367\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t123336714\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t125720143\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t126039427\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t127004913\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t128854935\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t128984541\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t134819118\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t135696903\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t137484210\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t137768001\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t138009297\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t138123566\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t138123699\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t139426142\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t146041529\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t147156352\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t148379180\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t148379362\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t148629281\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t150571560\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t152450338\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t152450519\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t16562058\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t16894872\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t17429367\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t20044401\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t26061110\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t26574315\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t28010205\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t30227710\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t30256558\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t35861923\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t56809068\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t87336398\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t88092779\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr7\t89920499\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t10576464\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t107426996\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t109087961\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t109275046\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t109334564\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t113806188\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t119851483\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t121354388\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t129127362\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t129549456\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t13548998\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t13668465\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t14306960\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t17594804\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t19919526\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t19924810\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t22870138\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t23921280\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t24206095\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t34068894\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t37107644\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t4586605\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t70850825\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t71717281\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t73173598\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t73183558\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t73297497\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t81256455\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t86143616\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t87180694\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t88126748\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t93828640\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr8\t97699878\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t100543647\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t103988283\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t106273656\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t107478162\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t108851463\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t110183808\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t111053664\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t116828689\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t118884586\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t120883928\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t123371104\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t13408238\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t14466849\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t14480293\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t24346538\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t3258857\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t42777363\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t43528251\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t43585984\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t44215148\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t44307103\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t54460731\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t66728918\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t66794084\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t67556540\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t70477636\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t72497695\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t72916030\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t74815214\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t75371664\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t8033087\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t8055015\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t83462792\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr9\t86714892\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t109484691\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t137172820\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t139917606\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t140401017\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t163589625\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t166360754\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t166427362\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t166432950\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t84483714\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chrX\t98516735\t.\t.\t.\t.\t.\t.\t.\t.\t.\n' |
| b |
| diff -r 000000000000 -r d9c1f2133124 tool-data/rnachipintegrator_canonical_genes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnachipintegrator_canonical_genes.loc.sample Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,19 @@ +#This is a sample file distributed with Galaxy that is used by the +#rnachipintegrator_canonical_genes tool. The file has this format (white space +#characters are TAB characters): +# +#<UniqueID> <Build> <Description> <PathToGeneListFile> +# +#For example: +# +#hg18_Gm12878_Ctcf hg18 Gm12878/Ctcf /genomes/hg18/Gm12878_Ctcf.tsv +#hg19_Gm12878_H3k27ac hg19 Gm12878/H3k27ac /genomes/hg19/Gm12878_H3k27ac.tsv +#mm9_Gm12878_H3k27me3 mm9 Gm12878/H3k27me3 /genomes/mm9/Gm12878_H3k27me3.tsv +#...etc... +# +#The gene list files should contain the gene symbol, chromosome, start and end +#positions, and strand for each gene in the list. +# +#This file should be placed in galaxy's tool-data directory when the +#rnachipintegrator_canonical_genes tool is installed. + |
| b |
| diff -r 000000000000 -r d9c1f2133124 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="rnachipintegrator_canonical_genes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/rnachipintegrator_canonical_genes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r d9c1f2133124 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 30 06:44:06 2015 -0400 |
| b |
| @@ -0,0 +1,74 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="python_xlwt" version="0.7.5"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/x/xlwt/xlwt-0.7.5.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Installs Python module xlwt 0.7.5</readme> + </package> + <package name="python_xlrd" version="0.9.3"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.3.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Installs Python module xlrd 0.9.3</readme> + </package> + <package name="python_xlutils" version="1.7.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/x/xlutils/xlutils-1.7.1.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Installs Python module xlutils 1.7.1</readme> + </package> + <package name="rnachipintegrator" version="0.4.4"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/fls-bioinformatics-core/RnaChipIntegrator/archive/v0.4.4.tar.gz</action> + <action type="move_file"> + <source>RnaChipIntegrator.py</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>Spreadsheet.py</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme>Installs RnaChipIntegrator 0.4.3</readme> + </package> +</tool_dependency> |