Mercurial > repos > iuc > dada2_makesequencetable

comparison README.md @ 1:9ccec6ed8e82 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
author iuc
date Thu, 05 Dec 2019 18:00:38 -0500
parents 6e0946238688
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0:6e0946238688 1:9ccec6ed8e82
1 Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html. 1 Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html.
2 2
3 - assignTaxonomyAddspecies
3 - filterAndTrim 4 - filterAndTrim
4 - learnErrors 5 - learnErrors
5 - dada 6 - dada
6 - mergePairs 7 - mergePairs
7 - makeSequenceTable 8 - makeSequenceTable
9 - plotComplexity
10 - plotQualityProfile
8 - removeBimeraDenovo 11 - removeBimeraDenovo
12 - seqCounts
9 13
10 Installation 14 Installation
11 ============ 15 ============
16
17 A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly.
12 18
13 The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases. 19 The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases.
14 In order to run the tools you may either upgrade Galaxy or execute the following two steps: 20 In order to run the tools you may either upgrade Galaxy or execute the following two steps:
15 21
16 1. `find GALAXY_ROOT/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ -name "dada2_*xml" -exec sed -i -e 's/profile="19.09"/profile="YOUR_RELEASE"/' {} ;` (replace GALAXY_ROOT and YOUR_RELEASE appropriately) 22 1. `find GALAXY_ROOT/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ -name "dada2_*xml" -exec sed -i -e 's/profile="19.09"/profile="YOUR_RELEASE"/' {} ;` (replace GALAXY_ROOT and YOUR_RELEASE appropriately)