k3yavi

import sys

##########################################################
#requires snakemake, python3, pyfasta to be installed
#save this file and provide all the binaries and their path
#in variables below.
#to run flux pipeline:
#snakemake run_flux_pipeline
#to run rsem pipeline:
#snakemake run_rsem_pipeline

k3yavi

```
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

#<Might have to write Yes and press enter>

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)"

brew install zsh

k3yavi

//from http://www.saltycrane.com/blog/2015/12/switching-emacs-vim-actually-spacemacs/

Useful Spacemacs commands

SPC q q - quit
SPC w / - split window vertically
SPC w - - split window horizontally
SPC 1   - switch to window 1
SPC 2   - switch to window 2
SPC w c - delete current window

k3yavi

https://www.youtube.com/watch?v=F0sRpgnFyMY

## Evil mode
/                       Start search in current buffer
n                       find next
N                       find previous
SPC s c                 clear the searches
:s/text/newtext/gc      Search and replace
SPC s h                 Symbol highlight + options for search, multiple edit,...

k3yavi

ALL = alevin.pdf
TEXFILES = alevin
# STYFILES = our-comments
CLSFILES = bmcart
FIGURES = figs/alevin.pdf figs/timing.pdf
LATEXMKOPTS = -pdf -dvi-
LATEX = pdflatex
BIBFILES = bmc_article

########### Shouldn't require configuration below here ##########

k3yavi

k3yavi

k3yavi

k3yavi

k3yavi

DATASETS = ["PBMC_8K", "PBMC_4k"]

SALMON = "$BINS/salmon-0.14.0_linux_x86_64/bin/salmon"

rule all:
  input: expand("quants/{dataset}/alevin/quants_mat.gz", dataset=DATASETS)

rule salmon_quant:
    input:
        r1 = "reads/{sample}_1.fastq",