Mercurial > repos > kevyin > fastq_groomer_parallel
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Sep 14 03:17:38 2012 -0400 @@ -0,0 +1,35 @@ +Copyright (c) 2012, Kenneth Sabir +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, are permitted provided +that the following conditions are met: + + - Redistributions of source code must retain the above copyright notice, this list of conditions and + the following disclaimer. + - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and + the following disclaimer in the documentation and/or other materials provided with the distribution. + - Neither the name of the Garvan Institute nor the names of its contributors may be used to endorse + or promote products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, +INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, +INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING +IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +################################################## +INSTALLATION: +#================================================# + +Set the number of threads to use by editing: +fastq_groomer_parallel.xml: +Modify the last argument in the <command> tag, Default is 8 + +Tested on galaxy-dist -r e6444e7a1685 +This currently depends on the following galaxy_utils python library which should come with the default galaxy install + +More info: + from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter +##################################################