App-Egaz

 view release on metacpan or  search on metacpan

Dockerfile  view on Meta::CPAN

        -libdir=$(brew --prefix)/Cellar/repeatmasker@4.1.1/4.1.1/libexec/Libraries \
        -trf_prgm=$(brew --prefix)/bin/trf \
        -default_search_engine=rmblast \
 && rm -fr $(brew --cache)/*

# R
RUN true \
 && export HOMEBREW_NO_ANALYTICS=1 \
 && export HOMEBREW_NO_AUTO_UPDATE=1 \
 && brew install r \
 && Rscript -e 'install.packages("extrafont", repos="http://cran.rstudio.com")' \
 && Rscript -e 'install.packages("VennDiagram", repos="http://cran.rstudio.com")' \
 && Rscript -e 'install.packages("ggplot2", repos="http://cran.rstudio.com")' \
 && Rscript -e 'install.packages("scales", repos="http://cran.rstudio.com")' \
 && Rscript -e 'install.packages("gridExtra", repos="http://cran.rstudio.com")' \
 && Rscript -e 'install.packages("readr", repos="http://cran.rstudio.com")' \
 && Rscript -e 'install.packages("ape", repos="http://cran.rstudio.com")' \
 && Rscript -e 'library(extrafont); font_import(prompt = FALSE); fonts();' \
 && rm -fr $(brew --cache)/*

WORKDIR /home/linuxbrew/App-Egaz
ADD . .

RUN true \
 && cpanm -nq https://github.com/wang-q/App-Plotr.git \
 && cpanm -nq --installdeps --with-develop . \
 && cpanm -nq . \
 && perl Build.PL \

share/circos.conf.tt2  view on Meta::CPAN

stroke_color     = dgrey
fill             = yes

# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.85r
show_label     = no
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 36

label_parallel   = yes

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 1

share/circos.conf.tt2  view on Meta::CPAN

    size           = 8p
    thickness      = 2p
    color          = black
    grid           = yes
    grid_color     = dgrey
    grid_thickness = 1p
</tick>

</ticks>

<<include etc/colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

share/plot_tree.R  view on Meta::CPAN

}

plot_tree <- function(tree) {
    barlen <- min(median(tree$edge.length), 0.1)
    if (barlen < 0.1)
        barlen <- 0.01
    tree <- ladderize(tree)
    plot.phylo(
        tree,
        cex = 0.8,
        font = 1,
        adj = 0,
        xpd = TRUE,
        label.offset = 0.001,
        no.margin = TRUE,
        underscore = TRUE
    )
    nodelabels(
        tree$node.label,
        adj = c(1.3,-0.5),
        frame = "n",
        cex = 0.8,
        font = 3,
        xpd = TRUE
    )
    add.scale.bar(cex = 0.8, lwd = 2, length = barlen)
}

pdf(file = opt$outfile)
tree <- read.tree(opt$infile)
plot_tree(tree)
dev.off()