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Michael Lovci mlovci

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mlovci / demonstration.ipynb
Last active August 29, 2015 14:04
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@mlovci
mlovci / test_overhaul.ipynb
Last active August 29, 2015 14:04
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@mlovci
mlovci / test_clipper.ipynb
Created July 29, 2014 02:15
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mlovci / variance_plotly.ipynb
Created August 13, 2014 19:23
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mlovci / gist:2adc03cc50c4cf3220fe
Last active August 29, 2015 14:06
download_sra.sh
#!/bin/bash
SRA=$1
mkdir dl_$SRA
cd dl_$SRA
echo downloading $SRA
DL_CMD="bionode-ncbi download sra $SRA"
echo $DL_CMD
eval $DL_CMD
find . | grep -P '.sra$'>sra_list
@mlovci
mlovci / run_notebook.sh
Created October 8, 2014 17:45
wrapper for ipython notebook
#!/bin/sh
ipython notebook --notebook-dir="~/ipython" --ip="*" --no-browser
@mlovci
mlovci / monocle_deps_installer.R
Last active August 29, 2015 14:07
install monocle dependencies
install.packages(c("VGAM", "irlba", "matrixStats", "igraph",
"combinat", "fastICA", "grid", "ggplot2", "Hmisc",
"reshape2", "plyr", "parallel", "methods"), repos='http://cran.us.r-project.org')
source("http://bioconductor.org/biocLite.R")
biocLite()
@mlovci
mlovci / muzak.py
Created October 14, 2014 19:55
def muzak(ob):
from IPython.display import HTML
from IPython.display import display
sound_tag = """
<audio controls autoplay>
<source src="http://k007.kiwi6.com/hotlink/9edy0q33fi/jazzy_elevator_music.mp3" type="audio/mpeg">
</audio>
"""
display(HTML(sound_tag))
@mlovci
mlovci / css.py
Last active August 29, 2015 14:07
pretty css
sekcss = """
<style>
.rendered_html
{
font-size: 140%;
line-height: 1.1;
margin: 0.5em 0;
}
@mlovci
mlovci / Dockerfile
Last active August 29, 2015 14:11
Minimal for Galaxy(docker) + IPython(docker)
FROM bgruening/galaxy-stable:dev
RUN git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/visualizations/ipython
ADD ./startup /usr/bin/startup
ADD ./clean.sh /usr/bin/clean.sh
RUN chmod 755 /usr/bin/startup && chmod 755 /usr/bin/clean.sh
RUN sudo apt-get install -y apache2
ADD ./apache_conf /apache_conf
RUN cat /apache_conf >> /etc/apache2/apache2.conf