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1 Copyright (c) 2012, Kenneth Sabir
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2 All rights reserved.
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4 Redistribution and use in source and binary forms, with or without modification, are permitted provided
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5 that the following conditions are met:
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7 - Redistributions of source code must retain the above copyright notice, this list of conditions and
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8 the following disclaimer.
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9 - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and
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10 the following disclaimer in the documentation and/or other materials provided with the distribution.
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11 - Neither the name of the Garvan Institute nor the names of its contributors may be used to endorse
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12 or promote products derived from this software without specific prior written permission.
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14 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
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15 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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16 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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17 INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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18 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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19 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
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20 IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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21
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22 ##################################################
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23 INSTALLATION:
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24 #================================================#
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25
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26 Set the number of threads to use by editing:
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27 fastq_groomer_parallel.xml:
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28 Modify the last argument in the <command> tag, Default is 8
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30 Tested on galaxy-dist -r e6444e7a1685
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31 This currently depends on the following galaxy_utils python library which should come with the default galaxy install
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33 More info:
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34 from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
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35 ##################################################
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