Mercurial > repos > frogs > frogs_3_1_0

view test-data/references/18-phylo_structure.log @ 0:59bc96331073 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
parents
children
line wrap: on
line source

## Application
Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py (version : 3.1)
Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py --varExp EnvType --ordination-method MDS --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/18-phylo_structure.html --log-file res/18-phylo_structure.log

########################################################################################################
# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
[1] "Rmarkdown version:  1.10"
[1] "Phyloseq version:  1.19.1")
Command:
	Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_structure.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/18-phylo_structure.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620190.28_24114_rmarkdown.stderr

Execution:
	start: 08 Feb 2019 11:03:14
	end:   08 Feb 2019 11:03:27

## Application
Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py (version : 3.1)
Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_structure.py --varExp EnvType --ordination-method MDS --rdata res/14-phylo_import.Rdata --distance-matrix res/Unifrac.tsv --html res/18-phylo_structure.html --log-file res/18-phylo_structure.log

########################################################################################################
# Run 1 code Rmarkdown (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
[1] "Rmarkdown version:  1.10"
[1] "Phyloseq version:  1.19.1")
Command:
	Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_structure.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/18-phylo_structure.html', params=list(data='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', varExp='EnvType',method='MDS',distance='/home/maria/workspace/git/FROGS/FROGS_master/test/res/Unifrac.tsv', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623069.52_25554_rmarkdown.stderr

Execution:
	start: 08 Feb 2019 11:51:12
	end:   08 Feb 2019 11:51:24