| Next changeset 1:02a01ea54722 (2016-07-26) |
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Commit message:
Uploaded initial version 2.1.0-4. |
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README.rst macs21_wrapper.py macs21_wrapper.xml test-data/test_MACS2.1.0_bw_html_report.zip test-data/test_MACS2.1.0_control_lambda.bdg test-data/test_MACS2.1.0_html_report.zip test-data/test_MACS2.1.0_peaks.xls test-data/test_MACS2.1.0_peaks.xls.re_match test-data/test_MACS2.1.0_peaks_narrowPeak.interval test-data/test_MACS2.1.0_summits.bed test-data/test_MACS2.1.0_treat_pileup.bdg test-data/test_MACS2.1.0_treat_pileup.bw test-data/test_region_IP.bed test-data/test_region_Input.bed tool_dependencies.xml |
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| diff -r 000000000000 -r 06cb587a5e87 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jun 30 08:16:18 2015 -0400 |
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| @@ -0,0 +1,99 @@ +MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling +================================================================== + +Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been +developed by Tao Lui +https://github.com/taoliu/MACS/ + +The reference for MACS is: + +- Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers + RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. + 2008;9(9):R137 + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take of installing the tool wrapper and +the MACS 2.1.0 program. + +Manual Installation +=================== + +There are two files to install: + +- ``macs21_wrapper.xml`` (the Galaxy tool definition) +- ``macs21_wrapper.py.sh`` (the Python script wrapper) + +The suggested location is in a ``tools/macs21/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the line: + + <tool file="macs21/macs21_wrapper.xml" /> + +You will also need to install MACS 2.1.0 and its dependencies: + +- https://pypi.python.org/pypi/MACS2 + +and ensure that it's on your Galaxy user's ``PATH`` when running the tool. + +If you want to run the functional tests, copy the sample test files under +sample test files under Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id macs2_wrapper + + +History +======= + +This tool was originally based on the ``modencode-dcc`` MACS2 tool developed +by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191`` +revision of the tool available via + +- http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 + +This version has been substantially modified both to adapt it to MACS 2.1.0, and +to re-implement the internal workings of the tool to conform with current +practices in invoking commands from Galaxy, and to add new functionality. + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +2.1.0-4 - Remove 'bdgcmp' functionality. +2.1.0-3 - Add tool tests +2.1.0-2 - Add option to create bigWig file from bedGraphs; fix bug with -B + option; make --mfold defaults consistent. +2.1.0-1 - Initial version +========== ====================================================================== + + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21 + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_macs21_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 06cb587a5e87 macs21_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs21_wrapper.py Tue Jun 30 08:16:18 2015 -0400 |
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| b'@@ -0,0 +1,262 @@\n+#!/bin/env python\n+#\n+# Galaxy wrapper to run MACS 2.1\n+#\n+# Completely rewritten from the original macs2 wrapped by Ziru Zhou\n+# taken from http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2\n+\n+import sys\n+import os\n+import subprocess\n+import tempfile\n+import shutil\n+\n+def move_file(working_dir,name,destination):\n+ """Move a file \'name\' from \'working_dir\' to \'destination\'\n+\n+ """\n+ if destination is None:\n+ # Nothing to do\n+ return\n+ source = os.path.join(working_dir,name)\n+ if os.path.exists(source):\n+ shutil.move(source,destination)\n+\n+def convert_xls_to_interval(xls_file,interval_file,header=None):\n+ """Convert MACS XLS file to interval\n+\n+ From the MACS readme: "Coordinates in XLS is 1-based which is different with\n+ BED format."\n+\n+ However this function no longer performs any coordinate conversions, it\n+ simply ensures that any blank or non-data lines are commented out\n+\n+ """\n+ fp = open(interval_file,\'wb\')\n+ if header:\n+ fp.write(\'#%s\\n\' % header)\n+ for line in open(xls_file):\n+ # Keep all existing comment lines\n+ if line.startswith(\'#\'):\n+ fp.write(line)\n+ else:\n+ # Split line into fields and test to see if\n+ # the \'start\' field is actually an integer\n+ fields = line.split(\'\\t\')\n+ if len(fields) > 1:\n+ try:\n+ int(fields[1])\n+ except ValueError:\n+ # Integer conversion failed so comment out\n+ # "bad" line instead\n+ fields[0] = "#%s" % fields[0]\n+ fp.write( \'\\t\'.join( fields ) )\n+ fp.close()\n+\n+def make_bigwig_from_bedgraph(bedgraph_file,bigwig_file,\n+ chrom_sizes,working_dir=None):\n+ """Make bigWig file from a bedGraph\n+\n+ The protocol is:\n+\n+ $ fetchChromSizes.sh mm9 > mm9.chrom.sizes\n+ $ bedClip treat.bedgraph mm9.chrom.sizes treat.clipped\n+ $ bedGraphToBigWig treat.clipped mm9.chrom.sizes treat.bw\n+\n+ Get the binaries from\n+ http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/\n+\n+ We skip the fetchChromSizes step if the \'chrom_sizes\'\n+ argument supplied a valid file with the chromosome sizes\n+ for the genome build in question.\n+\n+ """\n+ print "Generating bigWig from bedGraph..."\n+ # Check for chromosome sizes\n+ if not os.path.exists(chrom_sizes):\n+ # Determine genome build\n+ chrom_sizes = os.path.basename(chrom_sizes)\n+ genome_build = chrom_sizes.split(\'.\')[0]\n+ if genome_build == \'?\':\n+ # No genome build set\n+ sys.stderr.write("ERROR genome build not set, cannot get sizes for \'?\'\\n")\n+ sys.stderr.write("Assign a genome build to your input dataset and rerun\\n")\n+ sys.exit(1)\n+ print "Missing chrom sizes file, attempting to fetch for \'%s\'" % genome_build\n+ # Run fetchChromSizes\n+ chrom_sizes = os.path.join(working_dir,chrom_sizes)\n+ stderr_file = os.path.join(working_dir,"fetchChromSizes.stderr")\n+ cmd = "fetchChromSizes %s" % genome_build\n+ print "Running %s" % cmd\n+ proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir,\n+ stdout=open(chrom_sizes,\'wb\'),\n+ stderr=open(stderr_file,\'wb\'))\n+ proc.wait()\n+ # Copy stderr from fetchChromSizes for information only\n+ for line in open(stderr_file,\'r\'):\n+ print line.strip()\n+ os.remove(stderr_file)\n+ # Check that the sizes file was downloaded\n+ if not os.path.exists(chrom_sizes):\n+ sys.stderr.write("Failed to download chrom sizes for \'%s\'\\n" % genome_build)\n+ sys.exit(1)\n+ # Run bedClip\n+ treat_clipped = "%s.clipped" % os.path.basename(bedgraph_file)\n+ cmd = "bedClip %s %s %s" % (bedgraph_file,chrom_sizes,treat_clipped)\n+ print "Running %s" % cmd\n+ '..b'== \'--output-pileup\':\n+ output_treat_pileup = filen\n+ elif arg0 == \'--output-lambda-bedgraph\':\n+ output_lambda_bedgraph = filen\n+ elif arg0 == \'--output-bigwig\':\n+ output_bigwig = filen\n+ elif arg0 == \'--output-xls-to-interval\':\n+ output_xls_to_interval_peaks_file = filen\n+ elif arg0 == \'--output-peaks\':\n+ output_peaks = filen\n+ else:\n+ # Pass remaining args directly to MACS\n+ # command line\n+ cmdline.append(arg)\n+ \n+ cmdline = \' \'.join(cmdline)\n+ print "Generated command line:\\n%s" % cmdline\n+\n+ # Execute MACS2\n+ #\n+ # Make a working directory\n+ working_dir = tempfile.mkdtemp()\n+ #\n+ # Collect stderr in a file for reporting later\n+ stderr_filen = tempfile.NamedTemporaryFile().name\n+ #\n+ # Run MACS2\n+ proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir,\n+ stderr=open(stderr_filen,\'wb\'))\n+ proc.wait()\n+ \n+ # Run R script to create PDF from model script\n+ if os.path.exists(os.path.join(working_dir,"%s_model.r" % experiment_name)):\n+ cmdline = \'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"\' % \\\n+ (experiment_name, experiment_name)\n+ proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir)\n+ proc.wait()\n+\n+ # Convert XLS to interval, if requested\n+ if output_xls_to_interval_peaks_file is not None:\n+ peaks_xls_file = os.path.join(working_dir,\'%s_peaks.xls\' % experiment_name )\n+ if os.path.exists(peaks_xls_file):\n+ convert_xls_to_interval(peaks_xls_file,output_xls_to_interval_peaks_file,\n+ header=\'peaks file\')\n+\n+ # Create bigWig from bedGraph, if requested\n+ if output_bigwig is not None:\n+ treat_bedgraph_file = os.path.join(working_dir,\'%s_treat_pileup.bdg\' % experiment_name)\n+ if os.path.exists(treat_bedgraph_file):\n+ make_bigwig_from_bedgraph(treat_bedgraph_file,output_bigwig,\n+ chrom_sizes_file,working_dir)\n+ \n+ # Move MACS2 output files from working dir to their final destinations\n+ move_file(working_dir,"%s_summits.bed" % experiment_name,output_summits)\n+ move_file(working_dir,"%s_peaks.xls" % experiment_name,output_peaks)\n+ move_file(working_dir,"%s_peaks.narrowPeak" % experiment_name,output_narrowpeaks)\n+ move_file(working_dir,"%s_peaks.broadPeak" % experiment_name,output_broadpeaks)\n+ move_file(working_dir,"%s_peaks.gappedPeak" % experiment_name,output_gappedpeaks)\n+ move_file(working_dir,"%s_treat_pileup.bdg" % experiment_name,output_treat_pileup)\n+ move_file(working_dir,"%s_control_lambda.bdg" % experiment_name,output_lambda_bedgraph)\n+ move_file(working_dir,"bdgcmp_out.bdg",output_bdgcmp)\n+\n+ # Move remaining file to the \'extra files\' path and link from the HTML\n+ # file to allow user to access them from within Galaxy\n+ html_file = open(output_extra_html,\'wb\')\n+ html_file.write(\'<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\\n\' % experiment_name)\n+ # Make the \'extra files\' directory\n+ os.mkdir(output_extra_path)\n+ # Move the files\n+ for filen in sorted(os.listdir(working_dir)):\n+ shutil.move(os.path.join(working_dir,filen),\n+ os.path.join(output_extra_path,filen))\n+ html_file.write( \'<li><a href="%s">%s</a></li>\\n\' % (filen,filen))\n+ # All files moved, close out HTML\n+ html_file.write( \'</ul></p>\\n\' )\n+ # Append any stderr output\n+ html_file.write(\'<h3>Messages from MACS:</h3>\\n<p><pre>%s</pre></p>\\n\' %\n+ open(stderr_filen,\'rb\').read())\n+ html_file.write(\'</body></html>\\n\')\n+ html_file.close()\n+\n+ # Clean up the working directory and files\n+ os.unlink(stderr_filen)\n+ os.rmdir(working_dir)\n' |
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| diff -r 000000000000 -r 06cb587a5e87 macs21_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs21_wrapper.xml Tue Jun 30 08:16:18 2015 -0400 |
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| b'@@ -0,0 +1,398 @@\n+<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-4">\n+ <description>Model-based Analysis of ChIP-Seq: peak calling</description>\n+ <requirements>\n+ <requirement type="package" version="2.7">python</requirement>\n+ <requirement type="package" version="1.9">numpy</requirement>\n+ <requirement type="package" version="2.1.0.20140616">macs2</requirement>\n+ <requirement type="package" version="3.1.2">R</requirement>\n+ <requirement type="package" version="1.0">ucsc_tools_for_macs21</requirement>\n+ </requirements>\n+ <version_command>macs2 --version</version_command>\n+ <command interpreter="python">\n+ macs21_wrapper.py callpeak\n+ ##\n+ ## ChIP-seq input\n+ $input_chipseq_file1\n+ ##\n+ ## ChIP-seq control\n+ #if str($input_control_file1) != \'None\'\n+ -c $input_control_file1\n+ #end if\n+ ##\n+ --format=$input_chipseq_file1.extension\n+ --name="$experiment_name"\n+ --bw=$bw\n+ ##\n+ ## Genome size\n+ #if str($genome_size.gsize) == \'\'\n+ --gsize=$genome_size.user_defined_gsize\n+ #else:\n+ --gsize=$genome_size.gsize\n+ #end if\n+ ##\n+ ## Broad peaks\n+ #if str($broad_options.broad_regions) == \'broad\'\n+ --broad --broad-cutoff=$broad_options.broad_cutoff\n+ #end if\n+ ##\n+ ## (no)model options\n+ #if str($nomodel_type.nomodel_type_selector) == \'nomodel\'\n+ --nomodel --extsize=$nomodel_type.extsize\n+ #end if\n+ ##\n+ ## pq value select options\n+ #if str($pq_options.pq_options_selector) == \'qvalue\'\n+ --qvalue=$pq_options.qvalue\n+ #else\n+ --pvalue=$pq_options.pvalue\n+ #end if\n+ ##\n+ ## Bedgraph options\n+ #if $bdg_options.bdg\n+ -B $bdg_options.spmr\n+ #end if\n+ ##\n+ ## Advanced options\n+ #if $advanced_options.advanced_options_selector\n+ --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi\n+ $advanced_options.nolambda\n+ $advanced_options.call_summits\n+ #if str($advanced_options.keep_duplicates.keep_dup) == \'\'\n+ --keep-dup $advanced_options.keep_duplicates.maximum_tags\n+ #else\n+ --keep-dup $advanced_options.keep_duplicates.keep_dup\n+ #end if\n+ #else\n+ ## Defaults if advanced options not set\n+ --mfold 10 30 --keep-dup 1\n+ #end if\n+ ##\n+ ## Output files\n+ --output-summits=$output_summits_bed_file\n+ --output-extra-files=$output_extra_files\n+ --output-extra-files-path=$output_extra_files.files_path\n+ ##\n+ ## Narrow/broad peak outputs\n+ #if str($broad_options.broad_regions) == \'broad\'\n+ --output-broadpeaks=$output_broadpeaks_file\n+ --output-gappedpeaks=$output_gappedpeaks_file\n+ #else\n+ --output-narrowpeaks=$output_narrowpeaks_file\n+ #end if\n+ ##\n+ ## Bedgraph outputs\n+ #if $bdg_options.bdg\n+ --output-pileup=$output_treat_pileup_file \n+ --output-lambda-bedgraph=$output_lambda_bedgraph_file\n+ #if $bdg_options.make_bigwig\n+ --output-bigwig=$output_bigwig_file\n+ --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${input_chipseq_file1.dbkey}.len\n+ #end if\n+ #end if\n+ ##\n+ ## XLS/interval output\n+ #if str($xls_to_interval) == \'True\'\n+ --output-xls-to-interval=$output_xls_to_interval_peaks_file\n+ #else\n+ --output-peaks=$output_peaks_file\n+ #end if\n+ </command>\n+ <inputs>\n+ <!--experiment name used as base for output file names -->\n+ <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"\n+\t label="Experiment Name"/>\n+ <!--choose \'broad\' or \'narrow\' regions-->\n+ <conditional name="broad_options">\n+ <param name="broad_regions" type="select" label="Type of region to call"\n+\t help="Broad regions are formed by linking nearby enriched regions">\n+\t<option value="" selected="true">Narrow regions</option>\n+\t<option value="broad">Broad regions</option>\n+ </param>\n+ <when value="broad">\n+\t<param name="broad_cutoff" type="floa'..b'MACS2.1.0_treat_pileup.bdg" />\n+ <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />\n+ </test>\n+ <!-- Peak calling with bigwig output -->\n+ <test>\n+ <!-- Inputs -->\n+ <param name="experiment_name" value="test_MACS2.1.0" />\n+ <param name="broad_regions" value="" />\n+ <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3"\n+\t ftype="bed" />\n+ <param name="input_control_file1" value="test_region_Input.bed"\n+\t ftype="bed" />\n+ <param name="gsize" value="" />\n+ <param name="user_defined_gsize" value="775000000.0" />\n+ <param name="bw" value="300" />\n+ <param name="xls_to_interval" value="true" />\n+ <param name="bdg_options|bdg" value="-B" />\n+ <param name="bdg_options|spmr" value="--SPMR" />\n+ <param name="bdg_options|make_bigwig" value="true" />\n+ <param name="pq_options_selector" value="qvalue" />\n+ <param name="qvalue" value="0.05" />\n+ <param name="advanced_options_selector" value="true" />\n+ <param name="advanced_options|mfoldlo" value="5" />\n+ <param name="advanced_options|mfoldhi" value="50" />\n+ <param name="advanced_options|nolambda" value="" />\n+ <param name="advanced_options|call_summits" value="" />\n+ <param name="advanced_options|keep_duplicates" value="" />\n+ <param name="advanced_options|maximum_tags" value="1" />\n+ <param name="nomodel_type_selector" value="nomodel" />\n+ <param name="nomodel_type|extsize" value="243" />\n+ <!-- Outputs -->\n+ <output name="output_extra_files" file="test_MACS2.1.0_bw_html_report.zip"\n+\t compare="sim_size" delta="2500" />\n+ <output name="output_summits_bed_file" file="test_MACS2.1.0_summits.bed" />\n+ <output name="output_narrowpeaks_file" file="test_MACS2.1.0_peaks_narrowPeak.interval" />\n+ <output name="output_xls_to_interval_peaks_file"\n+\t file="test_MACS2.1.0_peaks.xls.re_match"\n+\t compare="re_match" lines_diff="1" />\n+ <output name="output_treat_pileup_file" file="test_MACS2.1.0_treat_pileup.bdg" />\n+ <output name="output_lambda_bedgraph_file" file="test_MACS2.1.0_control_lambda.bdg" />\n+ <output name="output_bigwig_file" file="test_MACS2.1.0_treat_pileup.bw"\n+\t compare="sim_size" />\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+MACS (Model-based Analysis of ChIP-seq) 2.1.0 provides algorithms for identifying\n+transcript factor binding sites. The program can be used either for ChIP-Seq data alone,\n+or with control sample data to improve specificity.\n+\n+View the MACS2 documentation at:\n+https://github.com/taoliu/MACS/blob/master/README.rst\n+\n+------\n+\n+**Usage**\n+\n+The tool interfaces with the **callpeak** function in MACS, which calls peaks from\n+alignment results.\n+\n+------\n+\n+**Credits**\n+\n+This Galaxy tool was based on the MACS2 tool hosted in the Galaxy toolshed at\n+\n+ * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2\n+\n+(specifically the 16:14f378e35191 revision of the tool) which is credited to Ziru\n+Zhou. This version is a reimplemented version developed within the Bioinformatics\n+Core Facility at the University of Manchester, which uses more up-to-date Galaxy\n+syntax and adds some extra features.\n+\n+The tool runs Tao Liu\'s MACS2 software:\n+\n+ * https://github.com/taoliu/MACS\n+\n+The reference for MACS is:\n+\n+ * Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C,\n+ Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS).\n+ Genome Biol. 2008;9(9):R137.\n+\n+Please kindly acknowledge both this Galaxy tool and the MACS2 package if you\n+use it.\n+ </help>\n+ <citations>\n+ <!--\n+ See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set\n+ Can be either DOI or Bibtex\n+ Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex\n+ -->\n+ <citation type="doi">10.1186/gb-2008-9-9-r137</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_control_lambda.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_control_lambda.bdg Tue Jun 30 08:16:18 2015 -0400 |
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| @@ -0,0 +1,153 @@ +chr26 0 4102915 0.31355 +chr26 4102915 4103978 486.00000 +chr26 4103978 4103998 972.00000 +chr26 4103998 4104449 1458.00000 +chr26 4104449 4105233 1944.00000 +chr26 4105233 4105326 2430.00000 +chr26 4105326 4105398 2916.00000 +chr26 4105398 4105644 3402.00024 +chr26 4105644 4105855 3888.00000 +chr26 4105855 4105980 4374.00000 +chr26 4105980 4106825 4860.00000 +chr26 4106825 4107471 5346.00049 +chr26 4107471 4107794 5832.00000 +chr26 4107794 4108037 20000.00000 +chr26 4108037 4108498 6804.00049 +chr26 4108498 4108857 9720.00000 +chr26 4108857 4108877 20000.00000 +chr26 4108877 4109100 40000.00000 +chr26 4109100 4109120 20000.00000 +chr26 4109120 4109327 14580.00000 +chr26 4109327 4109570 20000.00000 +chr26 4109570 4109733 8262.00000 +chr26 4109733 4109826 9720.00000 +chr26 4109826 4109898 14580.00000 +chr26 4109898 4109949 19440.00000 +chr26 4109949 4110111 14580.00000 +chr26 4110111 4110204 20000.00000 +chr26 4110204 4110276 40000.00000 +chr26 4110276 4110354 60000.00000 +chr26 4110354 4110447 40000.00000 +chr26 4110447 4110480 24300.00195 +chr26 4110480 4110733 29160.00000 +chr26 4110733 4110765 40000.00000 +chr26 4110765 4110826 24300.00195 +chr26 4110826 4110859 20000.00000 +chr26 4110859 4110976 40000.00000 +chr26 4110976 4111102 20000.00000 +chr26 4111102 4111144 14580.00000 +chr26 4111144 4111325 12150.00098 +chr26 4111325 4111355 14580.00000 +chr26 4111355 4111704 12636.00000 +chr26 4111704 4111947 20000.00000 +chr26 4111947 4112349 13608.00098 +chr26 4112349 4112592 20000.00000 +chr26 4112592 4112706 14580.00000 +chr26 4112706 4112862 20000.00000 +chr26 4112862 4112949 40000.00000 +chr26 4112949 4113105 20000.00000 +chr26 4113105 4113145 13608.00098 +chr26 4113145 4113327 14580.00000 +chr26 4113327 4113524 13608.00098 +chr26 4113524 4113767 20000.00000 +chr26 4113767 4113775 13608.00098 +chr26 4113775 4114145 14580.00000 +chr26 4114145 4114146 12636.00000 +chr26 4114146 4114154 20000.00000 +chr26 4114154 4114389 40000.00000 +chr26 4114389 4114686 24300.00195 +chr26 4114686 4114732 40000.00000 +chr26 4114732 4114855 60000.00000 +chr26 4114855 4114929 40000.00000 +chr26 4114929 4114975 20000.00000 +chr26 4114975 4115116 14580.00000 +chr26 4115116 4115234 19440.00000 +chr26 4115234 4115308 14580.00000 +chr26 4115308 4115326 12150.00098 +chr26 4115326 4115398 11664.00000 +chr26 4115398 4115495 11178.00000 +chr26 4115495 4115635 20000.00000 +chr26 4115635 4115837 24300.00195 +chr26 4115837 4115891 29160.00000 +chr26 4115891 4115990 40000.00000 +chr26 4115990 4116014 60000.00000 +chr26 4116014 4116072 80000.00000 +chr26 4116072 4116134 60000.00000 +chr26 4116134 4116215 40000.00000 +chr26 4116215 4116233 60000.00000 +chr26 4116233 4116257 40000.00000 +chr26 4116257 4116366 29160.00000 +chr26 4116366 4116450 34020.00000 +chr26 4116450 4116512 29160.00000 +chr26 4116512 4116611 24300.00195 +chr26 4116611 4116745 20000.00000 +chr26 4116745 4116831 40000.00000 +chr26 4116831 4116988 20000.00000 +chr26 4116988 4117136 11664.00000 +chr26 4117136 4117471 12150.00098 +chr26 4117471 4117730 11664.00000 +chr26 4117730 4117973 20000.00000 +chr26 4117973 4117983 11178.00000 +chr26 4117983 4118141 10692.00098 +chr26 4118141 4118645 11178.00000 +chr26 4118645 4118886 10692.00098 +chr26 4118886 4118904 11178.00000 +chr26 4118904 4119267 11664.00000 +chr26 4119267 4119275 11178.00000 +chr26 4119275 4119282 10692.00098 +chr26 4119282 4119525 20000.00000 +chr26 4119525 4119734 11178.00000 +chr26 4119734 4119808 10692.00098 +chr26 4119808 4119854 10206.00000 +chr26 4119854 4120286 9720.00000 +chr26 4120286 4120399 10206.00000 +chr26 4120399 4120642 20000.00000 +chr26 4120642 4120714 9720.00000 +chr26 4120714 4120957 20000.00000 +chr26 4120957 4120959 14580.00000 +chr26 4120959 4121021 19440.00000 +chr26 4121021 4121066 14580.00000 +chr26 4121066 4121216 19440.00000 +chr26 4121216 4121338 20000.00000 +chr26 4121338 4121445 40000.00000 +chr26 4121445 4121459 60000.00000 +chr26 4121459 4121581 40000.00000 +chr26 4121581 4121688 20000.00000 +chr26 4121688 4121837 19440.00000 +chr26 4121837 4121959 14580.00000 +chr26 4121959 4122015 9720.00000 +chr26 4122015 4122258 20000.00000 +chr26 4122258 4122851 8262.00000 +chr26 4122851 4123020 7776.00000 +chr26 4123020 4123263 20000.00000 +chr26 4123263 4123386 7776.00000 +chr26 4123386 4123404 9720.00000 +chr26 4123404 4123641 14580.00000 +chr26 4123641 4123764 9720.00000 +chr26 4123764 4123783 20000.00000 +chr26 4123783 4124007 40000.00000 +chr26 4124007 4124026 20000.00000 +chr26 4124026 4124386 14580.00000 +chr26 4124386 4124396 9720.00000 +chr26 4124396 4124639 20000.00000 +chr26 4124639 4124786 9234.00000 +chr26 4124786 4125017 9720.00000 +chr26 4125017 4125164 9234.00000 +chr26 4125164 4125407 20000.00000 +chr26 4125407 4125836 9234.00000 +chr26 4125836 4126337 8748.00000 +chr26 4126337 4126363 8262.00000 +chr26 4126363 4126459 9720.00000 +chr26 4126459 4126509 14580.00000 +chr26 4126509 4126699 19440.00000 +chr26 4126699 4126742 20000.00000 +chr26 4126742 4126837 40000.00000 +chr26 4126837 4126887 60000.00000 +chr26 4126887 4126942 80000.00000 +chr26 4126942 4126985 60000.00000 +chr26 4126985 4127080 40000.00000 +chr26 4127080 4127130 20000.00000 +chr26 4127130 4127320 19440.00000 +chr26 4127320 4127363 14580.00000 +chr26 4127363 4127459 9720.00000 +chr26 4127459 4127761 6804.00049 |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_html_report.zip |
| b |
| Binary file test-data/test_MACS2.1.0_html_report.zip has changed |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_peaks.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_peaks.xls Tue Jun 30 08:16:18 2015 -0400 |
| [ |
| @@ -0,0 +1,29 @@ +#peaks file +# This file is generated by MACS version 2.1.0.20140616 +# Command line: callpeak -t /home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_46.dat -c /home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_45.dat --format=BED --name=test_MACS2.1.0 --bw=300 --gsize=775000000.0 --nomodel --extsize=243 --qvalue=0.05 -B --SPMR --mfold 5 50 --keep-dup 1 +# ARGUMENTS LIST: +# name = test_MACS2.1.0 +# format = BED +# ChIP-seq file = ['/home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_46.dat'] +# control file = ['/home/pjb/BCF_Work/galaxies/test/galaxy-dist/database/files/000/dataset_45.dat'] +# effective genome size = 7.75e+08 +# band width = 300 +# model fold = [5, 50] +# qvalue cutoff = 5.00e-02 +# Larger dataset will be scaled towards smaller dataset. +# Range for calculating regional lambda is: 1000 bps and 10000 bps +# Broad region calling is off +# MACS will save fragment pileup signal per million reads + +# tag size is determined as 50 bps +# total tags in treatment: 50 +# tags after filtering in treatment: 50 +# maximum duplicate tags at the same position in treatment = 1 +# Redundant rate in treatment: 0.00 +# total tags in control: 50 +# tags after filtering in control: 50 +# maximum duplicate tags at the same position in control = 1 +# Redundant rate in control: 0.00 +# d = 243 +#chr start end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name +chr26 4118914 4119282 369 4119130 9.00 9.13132 6.31632 2.51561 test_MACS2.1.0_peak_1 |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_peaks.xls.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_peaks.xls.re_match Tue Jun 30 08:16:18 2015 -0400 |
| [ |
| @@ -0,0 +1,29 @@ +\#peaks\ file +\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.0\.20140616 +\#\ Command\ line\:\ callpeak\ \-t\ .* \-c\ .* \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.0\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1 +\#\ ARGUMENTS\ LIST\: +\#\ name\ \=\ test\_MACS2\.1\.0 +\#\ format\ \=\ BED +\#\ ChIP\-seq\ file\ \=\ \[\'.*\'\] +\#\ control\ file\ \=\ \[\'.*\'\] +\#\ effective\ genome\ size\ \=\ 7\.75e\+08 +\#\ band\ width\ \=\ 300 +\#\ model\ fold\ \=\ \[5\,\ 50\] +\#\ qvalue\ cutoff\ \=\ 5\.00e\-02 +\#\ Larger\ dataset\ will\ be\ scaled\ towards\ smaller\ dataset\. +\#\ Range\ for\ calculating\ regional\ lambda\ is\:\ 1000\ bps\ and\ 10000\ bps +\#\ Broad\ region\ calling\ is\ off +\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads + +\#\ tag\ size\ is\ determined\ as\ 50\ bps +\#\ total\ tags\ in\ treatment\:\ 50 +\#\ tags\ after\ filtering\ in\ treatment\:\ 50 +\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1 +\#\ Redundant\ rate\ in\ treatment\:\ 0\.00 +\#\ total\ tags\ in\ control\:\ 50 +\#\ tags\ after\ filtering\ in\ control\:\ 50 +\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1 +\#\ Redundant\ rate\ in\ control\:\ 0\.00 +\#\ d\ \=\ 243 +\#chr\ start\ end\ length\ abs\_summit\ pileup\ \-log10\(pvalue\)\ fold\_enrichment\ \-log10\(qvalue\)\ name +chr26\ 4118914\ 4119282\ 369\ 4119130\ 9\.00\ 9\.13132\ 6\.31632\ 2\.51561\ test\_MACS2\.1\.0\_peak\_1 |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_peaks_narrowPeak.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_peaks_narrowPeak.interval Tue Jun 30 08:16:18 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chr26 4118913 4119282 test_MACS2.1.0_peak_1 25 . 6.31632 9.13132 2.51561 216 |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_summits.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_summits.bed Tue Jun 30 08:16:18 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chr26 4119129 4119130 test_MACS2.1.0_peak_1 2.51561 |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_treat_pileup.bdg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_MACS2.1.0_treat_pileup.bdg Tue Jun 30 08:16:18 2015 -0400 |
| b |
| @@ -0,0 +1,100 @@ +chr26 0 4107561 0.00000 +chr26 4107561 4107804 20000.00000 +chr26 4107804 4108165 0.00000 +chr26 4108165 4108408 20000.00000 +chr26 4108408 4108531 0.00000 +chr26 4108531 4108774 20000.00000 +chr26 4108774 4109009 0.00000 +chr26 4109009 4109252 20000.00000 +chr26 4109252 4109506 0.00000 +chr26 4109506 4109749 20000.00000 +chr26 4109749 4109782 0.00000 +chr26 4109782 4110025 20000.00000 +chr26 4110025 4110080 0.00000 +chr26 4110080 4110323 20000.00000 +chr26 4110323 4111276 0.00000 +chr26 4111276 4111519 20000.00000 +chr26 4111519 4112110 0.00000 +chr26 4112110 4112353 20000.00000 +chr26 4112353 4112762 0.00000 +chr26 4112762 4113005 20000.00000 +chr26 4113005 4113579 0.00000 +chr26 4113579 4113822 20000.00000 +chr26 4113822 4113899 0.00000 +chr26 4113899 4114142 20000.00000 +chr26 4114142 4115021 0.00000 +chr26 4115021 4115264 20000.00000 +chr26 4115264 4115555 0.00000 +chr26 4115555 4115792 20000.00000 +chr26 4115792 4115798 40000.00000 +chr26 4115798 4116035 20000.00000 +chr26 4116035 4116615 0.00000 +chr26 4116615 4116858 20000.00000 +chr26 4116858 4116931 0.00000 +chr26 4116931 4116988 20000.00000 +chr26 4116988 4117174 40000.00000 +chr26 4117174 4117231 20000.00000 +chr26 4117231 4117308 0.00000 +chr26 4117308 4117551 20000.00000 +chr26 4117551 4117615 0.00000 +chr26 4117615 4117642 20000.00000 +chr26 4117642 4117737 40000.00000 +chr26 4117737 4117858 60000.00000 +chr26 4117858 4117885 40000.00000 +chr26 4117885 4117905 20000.00000 +chr26 4117905 4117980 40000.00000 +chr26 4117980 4118037 20000.00000 +chr26 4118037 4118122 40000.00000 +chr26 4118122 4118148 60000.00000 +chr26 4118148 4118280 40000.00000 +chr26 4118280 4118365 20000.00000 +chr26 4118365 4118516 0.00000 +chr26 4118516 4118531 20000.00000 +chr26 4118531 4118561 40000.00000 +chr26 4118561 4118753 60000.00000 +chr26 4118753 4118759 80000.00000 +chr26 4118759 4118774 60000.00000 +chr26 4118774 4118804 40000.00000 +chr26 4118804 4118812 20000.00000 +chr26 4118812 4118827 40000.00000 +chr26 4118827 4118852 60000.00000 +chr26 4118852 4118898 80000.00000 +chr26 4118898 4118913 100000.00000 +chr26 4118913 4118963 120000.00000 +chr26 4118963 4118967 140000.00000 +chr26 4118967 4118996 160000.00000 +chr26 4118996 4119022 140000.00000 +chr26 4119022 4119047 160000.00000 +chr26 4119047 4119055 180000.00000 +chr26 4119055 4119070 160000.00000 +chr26 4119070 4119077 140000.00000 +chr26 4119077 4119095 160000.00000 +chr26 4119095 4119103 140000.00000 +chr26 4119103 4119118 160000.00000 +chr26 4119118 4119141 180000.00000 +chr26 4119141 4119156 160000.00000 +chr26 4119156 4119163 140000.00000 +chr26 4119163 4119168 160000.00000 +chr26 4119168 4119206 180000.00000 +chr26 4119206 4119210 160000.00000 +chr26 4119210 4119265 140000.00000 +chr26 4119265 4119290 120000.00000 +chr26 4119290 4119320 100000.00000 +chr26 4119320 4119346 80000.00000 +chr26 4119346 4119361 60000.00000 +chr26 4119361 4119406 40000.00000 +chr26 4119406 4119411 20000.00000 +chr26 4119411 4122292 0.00000 +chr26 4122292 4122535 20000.00000 +chr26 4122535 4124351 0.00000 +chr26 4124351 4124452 20000.00000 +chr26 4124452 4124594 40000.00000 +chr26 4124594 4124695 20000.00000 +chr26 4124695 4125766 0.00000 +chr26 4125766 4125809 20000.00000 +chr26 4125809 4126009 40000.00000 +chr26 4126009 4126052 20000.00000 +chr26 4126052 4126452 0.00000 +chr26 4126452 4126695 20000.00000 +chr26 4126695 4127518 0.00000 +chr26 4127518 4127761 20000.00000 |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_MACS2.1.0_treat_pileup.bw |
| b |
| Binary file test-data/test_MACS2.1.0_treat_pileup.bw has changed |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_region_IP.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_region_IP.bed Tue Jun 30 08:16:18 2015 -0400 |
| b |
| @@ -0,0 +1,50 @@ +chr26 4107754 4107804 D3YGT8Q1:279:C6ND0ACXX:1:2307:11522:80910 255 - +chr26 4108358 4108408 D3YGT8Q1:279:C6ND0ACXX:1:1205:12295:24447 255 - +chr26 4108724 4108774 D3YGT8Q1:279:C6ND0ACXX:1:1212:7461:43211 255 - +chr26 4109009 4109059 D3YGT8Q1:279:C6ND0ACXX:1:2306:13509:41113 255 + +chr26 4109506 4109556 D3YGT8Q1:279:C6ND0ACXX:1:1316:8894:99440 255 + +chr26 4109975 4110025 D3YGT8Q1:279:C6ND0ACXX:1:1314:13929:4230 255 - +chr26 4110080 4110130 D3YGT8Q1:279:C6ND0ACXX:1:2116:20242:70310 255 + +chr26 4111276 4111326 D3YGT8Q1:279:C6ND0ACXX:1:1113:7893:68431 255 + +chr26 4112303 4112353 D3YGT8Q1:279:C6ND0ACXX:1:1312:10267:49823 255 - +chr26 4112955 4113005 D3YGT8Q1:279:C6ND0ACXX:1:1306:15218:93662 255 - +chr26 4113579 4113629 D3YGT8Q1:279:C6ND0ACXX:1:2101:12665:18403 255 + +chr26 4114092 4114142 D3YGT8Q1:279:C6ND0ACXX:1:2210:5952:64144 255 - +chr26 4115214 4115264 D3YGT8Q1:279:C6ND0ACXX:1:1214:9389:76439 255 - +chr26 4115748 4115798 D3YGT8Q1:279:C6ND0ACXX:1:1102:9329:33447 255 - +chr26 4115792 4115842 D3YGT8Q1:279:C6ND0ACXX:1:1209:7255:23188 255 + +chr26 4116615 4116665 D3YGT8Q1:279:C6ND0ACXX:1:2203:17446:35897 255 + +chr26 4116988 4117038 D3YGT8Q1:279:C6ND0ACXX:1:2203:8076:21265 255 + +chr26 4117124 4117174 D3YGT8Q1:279:C6ND0ACXX:1:1210:4683:41907 255 - +chr26 4117501 4117551 D3YGT8Q1:279:C6ND0ACXX:1:1112:18900:56439 255 - +chr26 4117615 4117665 D3YGT8Q1:279:C6ND0ACXX:1:2313:2299:78456 255 + +chr26 4117835 4117885 D3YGT8Q1:279:C6ND0ACXX:1:2107:13997:60524 255 - +chr26 4117905 4117955 D3YGT8Q1:279:C6ND0ACXX:1:2201:10479:92578 255 + +chr26 4117930 4117980 D3YGT8Q1:279:C6ND0ACXX:1:2110:14632:99394 255 - +chr26 4118037 4118087 D3YGT8Q1:279:C6ND0ACXX:1:1104:14470:25800 255 + +chr26 4118122 4118172 D3YGT8Q1:279:C6ND0ACXX:1:2115:11588:70088 255 + +chr26 4118709 4118759 D3YGT8Q1:279:C6ND0ACXX:1:1216:4958:48081 255 - +chr26 4118724 4118774 D3YGT8Q1:279:C6ND0ACXX:1:1103:19280:11053 255 - +chr26 4118753 4118803 D3YGT8Q1:279:C6ND0ACXX:1:1109:5242:36011 255 + +chr26 4118754 4118804 D3YGT8Q1:279:C6ND0ACXX:1:2115:21104:40586 255 - +chr26 4118852 4118902 D3YGT8Q1:279:C6ND0ACXX:1:2106:20411:76655 255 + +chr26 4118963 4119013 D3YGT8Q1:279:C6ND0ACXX:1:1115:12391:82672 255 + +chr26 4118967 4119017 D3YGT8Q1:279:C6ND0ACXX:1:1316:6521:21414 255 + +chr26 4119005 4119055 D3YGT8Q1:279:C6ND0ACXX:1:2304:6533:74899 255 - +chr26 4119020 4119070 D3YGT8Q1:279:C6ND0ACXX:1:2305:4205:52717 255 - +chr26 4119022 4119072 D3YGT8Q1:279:C6ND0ACXX:1:2209:3941:33541 255 + +chr26 4119047 4119097 D3YGT8Q1:279:C6ND0ACXX:1:1311:20210:42351 255 + +chr26 4119091 4119141 D3YGT8Q1:279:C6ND0ACXX:1:2106:1249:92735 255 - +chr26 4119106 4119156 D3YGT8Q1:279:C6ND0ACXX:1:2214:19237:88451 255 - +chr26 4119168 4119218 D3YGT8Q1:279:C6ND0ACXX:1:1205:5997:59335 255 + +chr26 4119270 4119320 D3YGT8Q1:279:C6ND0ACXX:1:1203:19488:98141 255 - +chr26 4119296 4119346 D3YGT8Q1:279:C6ND0ACXX:1:1215:19021:97547 255 - +chr26 4119311 4119361 D3YGT8Q1:279:C6ND0ACXX:1:1106:19108:19961 255 - +chr26 4119356 4119406 D3YGT8Q1:279:C6ND0ACXX:1:2108:17061:18071 255 - +chr26 4122292 4122342 D3YGT8Q1:279:C6ND0ACXX:1:2105:6803:72755 255 + +chr26 4124452 4124502 D3YGT8Q1:279:C6ND0ACXX:1:2303:8935:84202 255 + +chr26 4124544 4124594 D3YGT8Q1:279:C6ND0ACXX:1:1115:5982:45995 255 - +chr26 4125766 4125816 D3YGT8Q1:279:C6ND0ACXX:1:1214:15854:88292 255 + +chr26 4126002 4126052 D3YGT8Q1:279:C6ND0ACXX:1:1106:12069:84969 255 - +chr26 4126452 4126502 D3YGT8Q1:279:C6ND0ACXX:1:1301:4389:93421 255 + +chr26 4127711 4127761 D3YGT8Q1:279:C6ND0ACXX:1:1314:2721:99427 255 - |
| b |
| diff -r 000000000000 -r 06cb587a5e87 test-data/test_region_Input.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_region_Input.bed Tue Jun 30 08:16:18 2015 -0400 |
| b |
| @@ -0,0 +1,50 @@ +chr26 4107915 4107965 D3YGT8Q1:279:C6ND0ACXX:1:2205:7723:65712 255 + +chr26 4108978 4109028 D3YGT8Q1:279:C6ND0ACXX:1:2111:18182:78807 255 + +chr26 4108998 4109048 D3YGT8Q1:279:C6ND0ACXX:1:1102:16043:23843 255 + +chr26 4109399 4109449 D3YGT8Q1:279:C6ND0ACXX:1:2215:2801:57221 255 - +chr26 4110183 4110233 D3YGT8Q1:279:C6ND0ACXX:1:1315:19316:26775 255 - +chr26 4110276 4110326 D3YGT8Q1:279:C6ND0ACXX:1:1314:1280:77850 255 - +chr26 4110348 4110398 D3YGT8Q1:279:C6ND0ACXX:1:1216:4159:61939 255 - +chr26 4110594 4110644 D3YGT8Q1:279:C6ND0ACXX:1:1312:5546:70647 255 - +chr26 4110805 4110855 D3YGT8Q1:279:C6ND0ACXX:1:2210:12809:70996 255 - +chr26 4110980 4111030 D3YGT8Q1:279:C6ND0ACXX:1:2215:3014:41883 255 + +chr26 4111825 4111875 D3YGT8Q1:279:C6ND0ACXX:1:2314:17556:68202 255 + +chr26 4112421 4112471 D3YGT8Q1:279:C6ND0ACXX:1:1204:13331:57729 255 - +chr26 4112827 4112877 D3YGT8Q1:279:C6ND0ACXX:1:2309:11398:71181 255 + +chr26 4112983 4113033 D3YGT8Q1:279:C6ND0ACXX:1:1104:16671:54740 255 + +chr26 4113645 4113695 D3YGT8Q1:279:C6ND0ACXX:1:2212:20179:47885 255 + +chr26 4114267 4114317 D3YGT8Q1:279:C6ND0ACXX:1:2314:3773:63068 255 + +chr26 4114275 4114325 D3YGT8Q1:279:C6ND0ACXX:1:1116:18465:6326 255 + +chr26 4114684 4114734 D3YGT8Q1:279:C6ND0ACXX:1:1114:17981:44317 255 - +chr26 4114758 4114808 D3YGT8Q1:279:C6ND0ACXX:1:1103:15929:31123 255 - +chr26 4114804 4114854 D3YGT8Q1:279:C6ND0ACXX:1:1208:10693:22578 255 - +chr26 4115616 4115666 D3YGT8Q1:279:C6ND0ACXX:1:1101:1142:17054 255 + +chr26 4115950 4116000 D3YGT8Q1:279:C6ND0ACXX:1:1316:13040:39630 255 + +chr26 4116012 4116062 D3YGT8Q1:279:C6ND0ACXX:1:2107:20439:44058 255 + +chr26 4116111 4116161 D3YGT8Q1:279:C6ND0ACXX:1:2307:1504:41529 255 + +chr26 4116135 4116185 D3YGT8Q1:279:C6ND0ACXX:1:2210:2837:7759 255 + +chr26 4116287 4116337 D3YGT8Q1:279:C6ND0ACXX:1:2313:15422:100876 255 - +chr26 4116709 4116759 D3YGT8Q1:279:C6ND0ACXX:1:2301:13318:45125 255 + +chr26 4116866 4116916 D3YGT8Q1:279:C6ND0ACXX:1:1113:1326:96268 255 + +chr26 4117851 4117901 D3YGT8Q1:279:C6ND0ACXX:1:1310:2843:93758 255 + +chr26 4119403 4119453 D3YGT8Q1:279:C6ND0ACXX:1:1304:17211:28405 255 + +chr26 4120471 4120521 D3YGT8Q1:279:C6ND0ACXX:1:2116:18127:100146 255 - +chr26 4120786 4120836 D3YGT8Q1:279:C6ND0ACXX:1:1207:2164:6021 255 - +chr26 4121337 4121387 D3YGT8Q1:279:C6ND0ACXX:1:2215:9085:93015 255 + +chr26 4121459 4121509 D3YGT8Q1:279:C6ND0ACXX:1:2311:16000:27081 255 + +chr26 4121566 4121616 D3YGT8Q1:279:C6ND0ACXX:1:1216:18410:44768 255 + +chr26 4122136 4122186 D3YGT8Q1:279:C6ND0ACXX:1:2316:17558:30500 255 + +chr26 4123141 4123191 D3YGT8Q1:279:C6ND0ACXX:1:2203:15835:86872 255 + +chr26 4123836 4123886 D3YGT8Q1:279:C6ND0ACXX:1:2212:16650:8391 255 - +chr26 4123904 4123954 D3YGT8Q1:279:C6ND0ACXX:1:1307:7349:80960 255 + +chr26 4124517 4124567 D3YGT8Q1:279:C6ND0ACXX:1:1213:6010:82097 255 + +chr26 4125236 4125286 D3YGT8Q1:279:C6ND0ACXX:1:2216:1172:30684 255 - +chr26 4126820 4126870 D3YGT8Q1:279:C6ND0ACXX:1:2107:12500:48771 255 + +chr26 4126863 4126913 D3YGT8Q1:279:C6ND0ACXX:1:2105:1028:78112 255 + +chr26 4126909 4126959 D3YGT8Q1:279:C6ND0ACXX:1:1302:19618:57506 255 - +chr26 4126959 4127009 D3YGT8Q1:279:C6ND0ACXX:1:1204:9666:55269 255 - +chr26 4128534 4128584 D3YGT8Q1:279:C6ND0ACXX:1:2312:9851:2880 255 + +chr26 4129060 4129110 D3YGT8Q1:279:C6ND0ACXX:1:2104:4039:10225 255 + +chr26 4129077 4129127 D3YGT8Q1:279:C6ND0ACXX:1:1306:15379:11481 255 + +chr26 4129446 4129496 D3YGT8Q1:279:C6ND0ACXX:1:1303:9852:6188 255 + +chr26 4130521 4130571 D3YGT8Q1:279:C6ND0ACXX:1:1201:20815:69132 255 + |
| b |
| diff -r 000000000000 -r 06cb587a5e87 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 30 08:16:18 2015 -0400 |
| b |
| @@ -0,0 +1,65 @@ +<?xml version="1.0"?> +<tool_dependency> + <!-- Dependencies from main/test toolsheds --> + <package name="numpy" version="1.9"> + <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.1.2"> + <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <!-- Subset of UCSC tools --> + <package name="ucsc_tools_for_macs21" version="1.0"> + <install version="1.0"> + <actions> + <!-- fetchChromSizes --> + <action type="download_binary"> + <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template> + </action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/fetchChromSizes</file> + </action> + <!-- bedClip --> + <action type="download_binary"> + <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template> + </action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/bedClip</file> + </action> + <!-- bedGraphToBigWig --> + <action type="download_binary"> + <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template> + </action> + <action type="chmod"> + <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> + <!-- MACS 2.1.0 --> + <package name="macs2" version="2.1.0.20140616"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action> + <!-- Install environment for main & test toolsheds --> + <action type="set_environment_for_install"> + <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.9" /> + </repository> + </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>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme> + </package> +</tool_dependency> |