Avi Srivastava k3yavi
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| 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
/ Non-admin Installs
Last active
June 21, 2016 20:13
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| ``` | |
| 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
/ spacemacs-cheatsheet.txt
Last active
February 28, 2024 01:15
— forked from davoclavo/spacemacs-cheatsheet.md
Spacemacs cheatsheet
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| //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
/ spacemacs-keybindings.txt
Created
May 16, 2017 23:12
— forked from Softsapiens/spacemacs-keybindings.txt
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| 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,... |
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| 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
/ alevin-default.ipynb
Last active
July 11, 2019 20:35
Example pipeline for Alevin-tool on 10x-pbmc 1k data.
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k3yavi
/ merge.ipynb
Last active
October 27, 2018 20:07
Depth Normalization of Alevin generated counts on multiple libraries.
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k3yavi
/ loading.ipynb
Created
February 7, 2019 23:31
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k3yavi
/ alevin.snk
Created
June 7, 2019 17:12
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| 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", |
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