Mercurial > repos > kevyin > fastq_groomer_parallel
changeset 17:cc357aad2022
Merge heads at 15:9b6eee0346de and 16:42f66e55b26b which were created as a result of a recently fixed bug.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Mon, 13 Jan 2014 12:26:39 -0500 |
| parents | 42f66e55b26b (diff) 9b6eee0346de (current diff) |
| children | 954a6dea0561 |
| files | README fastq_groomer_parallel.xml |
| diffstat | 2 files changed, 22 insertions(+), 15 deletions(-) [+] |
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--- a/README Thu Sep 13 22:01:55 2012 -0400 +++ b/README Mon Jan 13 12:26:39 2014 -0500 @@ -1,30 +1,37 @@ 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: +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. + - 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. +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: +INSTALLATION: #================================================# Set the number of threads to use edit fastq_groomer_parallel.xml: Modify the last argument in the <command> tag, Default is 2 -Tested on -r e6444e7a1685 +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:
--- a/fastq_groomer_parallel.xml Thu Sep 13 22:01:55 2012 -0400 +++ b/fastq_groomer_parallel.xml Mon Jan 13 12:26:39 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="fastq_groomer_parallel" name="FASTQ Parallel Groomer" version="0.3.0"> +<tool id="fastq_groomer_parallel" name="FASTQ Parallel Groomer" version="0.3.1"> <description>Parallel Implementation of FASTQ Groomer</description> <command interpreter="python">fastq_groomer_parallel.py '$input_file' '$input_type' '$output_file' #if str( $options_type['options_type_selector'] ) == 'basic':