https://github.com/eco32i/bash_kernel
Follow the instructions in the repo. Don't forget to activate your environment before installing.
This fork will produce incremental output when run inside jupyter notebook. The original kernel waits until the cell execution is done and then outputs all at once.
For Mac OS:
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wget https://github.com/pachterlab/kallisto/releases/download/v0.43.0/kallisto_mac-v0.43.0.tar.gz
For linux:
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wget https://github.com/pachterlab/kallisto/releases/download/v0.43.0/kallisto_linux-v0.43.0.tar.gz
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%%bash
mv kallisto_linux-v0.43.0.tar.gz ~/bin
cd ~/bin
tar -xzvf kallisto_linux-v0.43.0.tar.gz
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wget -P ../data http://bio.math.berkeley.edu/kallisto/transcriptomes/Caenorhabditis_elegans.WBcel235.rel79.cdna.all.fa.gz
Install R kernel for jupyter
You'll need to install R first if it's not installed on your system. The easiest way is to use conda.
Then follow the instructions on sleuth github repo to complete the installation.
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#dirs="lo05 lo09 lo03 lo11"
dirs="lo11"
for d in $dirs
do
mkdir ../data/$d
wget -P ../data/$d http://lab.nudlerlab.info/data/$d/R1.fastq.gz
wget -P ../data/$d http://lab.nudlerlab.info/data/$d/R2.fastq.gz
#mv $d ../data
done
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ls ../data | grep ^lo
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ls -lah ../data
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