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#!/bin/bash

set -euo pipefail

wget \
  --recursive \
  -O /dev/stdout \
  "ftp://ftp.ncbi.nih.gov/refseq/release/complete/*genomic*.fna.gz" \
  > refseq_complete.fa.gz

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fastqc_delzip () {
	fastqc --nogroup -f fastq $1
	rm *_fastqc.zip
}

alias fastqc2='fastqc_delzip'

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#!/bin/bash

for i in *fna
do
  echo $i
  blastn \
    -query $i \
    -db nt \
    -out $(basename $i).blastn \
    -outfmt "6 qseqid sseqid qstart qend sstart send score length pident nident evalue salltitles" \

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#!/bin/bash

R -e "install.packages(c('agricolae', 'gam', 'gamlss', 'gbm', 'glmnet', 'inlinedocs', 'logging', 'MASS', 'nlme', 'optparse', 'outliers', 'penalized', 'pscl', 'robustbase', 'pheatmap', 'ggplot2', 'cowplot'), repos='http://cran.r-project.org')"
wget https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.4.tar.gz
R CMD INSTALL Maaslin_0.0.4.tar.gz
rm Maaslin_0.0.4.tar.gz

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#!/bin/env ruby 

p "ibqqz!cjsuiebz!Wjdups".chars.map {|c| (c.ord-1).chr}.join 

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#!/bin/bash
# -------------------------------------------------------------------------------------
#
cd $HOME/bin && \
wget http://downloads.webmproject.org/releases/webp/libwebp-0.4.3.tar.gz && \
tar -xvzf libwebp-0.4.3.tar.gz && \
cd libwebp-0.4.3 && \
./configure --prefix=/usr/local/libwebp-0.4.3 && \
make && sudo make install && cd /usr/local && \
sudo ln -s libwebp-0.4.3 libwebp && \

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sudo curl -sL https://deb.nodesource.com/setup_10.x | sudo bash -
sudo apt-get install -y nodejs

npm config list

__='
; cli configs
metrics-registry = "https://registry.npmjs.org/"
scope = ""
user-agent = "npm/6.4.1 node/v10.15.3 linux x64"

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RealPoint[p_] := p[[1 ;; 3]]/p[[4]];

PluckerLine[{a_, b_}] := Module[{safeA, safeB},
   safeA = If[a[[4]] == 0, a + b, a];
   safeB = If[b[[4]] == 0, a + b, b];
   InfiniteLine[RealPoint /@ {safeA, safeB}]];

FamilyFromVerts[V_] := 
  Map[Transpose, 
   Map[{Re[#], Im[#]} &, 

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DynamicModule[{cols, r, u, verts},
 cols = RGBColor /@ {"#35342f", "#f1f2f0"};
 Manipulate[
  r = 1/2 - Cos[s]/2;
  u = If[s < π, s, s + 2 π];
  verts = 
   Table[(1 - r (-1)^(If[s < π, i + 1, i])) {Cos[
       2 π i/8 - u/8 - π/8], 
      Sin[2 π i/8 - u/8 - π/8]}, {i, 0, 7}];
  Graphics[{Thickness[.005], CapForm["Round"], cols[[1]], 

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DynamicModule[{n = 8, k = 6, r, cols, verts},
 cols = RGBColor /@ {"#00ADB5", "#EEEEEE", "#FF5722", "#303841"};
 Manipulate[
  r = Cos[s];
  verts = 
   Table[(1 - r (-1)^(i + 1)) {Cos[2 π i/n - π (r + 1)/8], 
      Sin[2 π i/n - π (r + 1)/8]}, {i, 0, n - 1}];
  Graphics[{Thickness[.0075], CapForm["Round"], Opacity[.8], 
    Table[{Blend[cols[[;; 3]], 1 - Abs[11/5 t - 11/10]], 
      Line[{t verts[[i]] + (1 - t) RotateRight[verts, 3][[i]],