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zorbax / install_melonpann.sh
Created April 27, 2020 12:20
( conda create -y -n "melonpann" && source activate "melonpann" && \
conda install r-base=3.5.0 r-devtools r-fbasics -yc r && \
R -q -e "install.packages('BiocManager', repos='http://cran.r-project.org'); \
library('BiocManager'); BiocManager::install('ccrepe');" && \
R -q -e "install.packages('optparse', repos='http://cran.r-project.org')" && \
R -q -e "install.packages('AssocTests', repos='http://cran.r-project.org')" && \
R -q -e "install.packages('glmnet', repos='http://cran.r-project.org')" && \
R -q -e "install.packages('HDtweedie', repos='http://cran.r-project.org')" && \
R -q -e "install.packages('getopt', repos='http://cran.r-project.org')" && \
R -q -e "install.packages('doParallel', repos='http://cran.r-project.org')" && \
@zorbax
zorbax / install_rvm.sh
Created September 16, 2019 21:48
#!/bin/bash
key1="409B6B1796C275462A1703113804BB82D39DC0E3"
key2="7D2BAF1CF37B13E2069D6956105BD0E739499BDB"
gpg2 --keyserver hkp://pool.sks-keyservers.net --recv-keys $key1 $key2
curl -sSL https://get.rvm.io | bash
source $HOME/.rvm/scripts/rvm
echo "rvm_autoupdate_flag=0" >> ~/.rvmrc
echo "rvm_autoupdate_flag=2" >> ~/.rvmrc
@zorbax
zorbax / singularity_installation.sh
Last active September 15, 2019 02:21
sudo apt-get update && sudo apt-get install -y \
build-essential libssl-dev uuid-dev libgpgme11-dev \
squashfs-tools libseccomp-dev pkg-config
export VERSION=1.11 OS=linux ARCH=amd64 && \
wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
tar -C $HOME/bin -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
rm go$VERSION.$OS-$ARCH.tar.gz
echo 'export PATH=${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
@zorbax
zorbax / filterL6.sh
Created May 23, 2019 03:56
#!/bin/bash
usage ()
{
echo ""
echo "Usage : `basename $0` <tableL6.txt> <L6_clean.tsv>"
echo ""
exit
}
if [ "$1" = "" ]; then
@zorbax
zorbax / parametric_tests.py
Created March 18, 2019 20:14
#!/usr/bin/env python
from numpy.random import seed
from numpy.random import randn
from numpy import mean
from numpy import std
from scipy.stats import ttest_ind
from scipy.stats import ttest_rel
from scipy.stats import f_oneway
@zorbax
zorbax / nonparametric_tests.py
Created March 11, 2019 08:18
#!/usr/bin/env python3
from numpy.random import seed
from numpy.random import randn
from numpy import mean
from numpy import std
from scipy.stats import mannwhitneyu
from scipy.stats import wilcoxon
from scipy.stats import kruskal
from scipy.stats import friedmanchisquare
@zorbax
zorbax / normality_tests.py
Created March 11, 2019 08:14
#!/usr/bin/env python3
from numpy.random import seed
from numpy.random import randn
from numpy import mean
from numpy import std
import matplotlib.pyplot as plt
from statsmodels.graphics.gofplots import qqplot
from scipy.stats import shapiro
@zorbax
zorbax / Strain_Senterica.tsv
Created March 7, 2019 19:58
ST aroC dnaN hemD hisD purE sucA thrA SEROTYPE eBG
1 1 1 1 1 1 1 5 Typhi 13
2 1 1 2 1 1 1 5 Typhi 13
3 1 1 2 1 1 1 9 Typhi 13
4 43 41 16 13 34 13 4 Montevideo 40
5 16 43 45 43 36 39 42 Newport 2
6 4 4 4 5 4 4 8 Enteritidis
7 2 2 3 2 2 2 6 99
8 1 1 2 3 1 1 5 Typhi 13
9 33 26 30 55 21 87 134 220
@zorbax
zorbax / install_sratoolkit.sh
Created November 8, 2018 17:22
cd $HOME/bin
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz
tar -zxvf sratoolkit.2.9.2-ubuntu64.tar.gz && rm sratoolkit.2.9.2-ubuntu64.tar.gz
mv sratoolkit.2.9.2-ubuntu64 sratoolkit.2.9.2
find sratoolkit.2.9.2 -type l -name "fastq-dump" -exec ln -s {} . \;
@zorbax
zorbax / aln.converter.pl
Created November 7, 2018 17:43
#!/usr/bin/env perl
#
# @author: Luis M. Rodriguez-R
# @update: Mar-23-2015
# @license: artistic license 2.0
#
use Bio::AlignIO;