Mercurial > repos > kevyin > fastq_groomer_parallel
comparison README @ 2:cac848910bd8
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| author | kevyin |
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| date | Fri, 14 Sep 2012 03:17:38 -0400 |
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| 1:2f394cd7db91 | 2:cac848910bd8 |
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| 1 Copyright (c) 2012, Kenneth Sabir | |
| 2 All rights reserved. | |
| 3 | |
| 4 Redistribution and use in source and binary forms, with or without modification, are permitted provided | |
| 5 that the following conditions are met: | |
| 6 | |
| 7 - Redistributions of source code must retain the above copyright notice, this list of conditions and | |
| 8 the following disclaimer. | |
| 9 - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and | |
| 10 the following disclaimer in the documentation and/or other materials provided with the distribution. | |
| 11 - Neither the name of the Garvan Institute nor the names of its contributors may be used to endorse | |
| 12 or promote products derived from this software without specific prior written permission. | |
| 13 | |
| 14 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, | |
| 15 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| 16 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, | |
| 17 INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | |
| 18 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | |
| 19 THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING | |
| 20 IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | |
| 21 | |
| 22 ################################################## | |
| 23 INSTALLATION: | |
| 24 #================================================# | |
| 25 | |
| 26 Set the number of threads to use by editing: | |
| 27 fastq_groomer_parallel.xml: | |
| 28 Modify the last argument in the <command> tag, Default is 8 | |
| 29 | |
| 30 Tested on galaxy-dist -r e6444e7a1685 | |
| 31 This currently depends on the following galaxy_utils python library which should come with the default galaxy install | |
| 32 | |
| 33 More info: | |
| 34 from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter | |
| 35 ################################################## |