mfansler

#!/usr/bin/env conda run -n base --no-capture-output python                                                                                                  

## Usage: conda-list-any.py [PACKAGE ...]                                                                                                                    
## Example: conda-list-any.py numpy pandas                                                                                                                   

import conda.gateways.logging
from conda.core.envs_manager import list_all_known_prefixes
from conda.cli.main_list import list_packages
from conda.common.compat import text_type
import sys

mfansler

package main

import (
       "fmt"

       "math"
       
       "gonum.org/v1/gonum/stat/distuv"
)

mfansler

name: so-ipopt
channels:
  - conda-forge
  - defaults
dependencies:
  - pyomo
  - ipopt

mfansler

name: foo
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - _r-mutex=1.0.1=anacondar_1
  - binutils_impl_linux-64=2.35=h18a2f87_9

mfansler

name: so-seurat
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _r-mutex=1.0.1=anacondar_1
  - bwidget=1.9.14=0
  - bzip2=1.0.8=haf1e3a3_3
  - c-ares=1.16.1=haf1e3a3_3

mfansler

#!/usr/bin/env awk -f
#' Author: Mervin Fansler
#' GitHub: @mfansler
#' License: MIT
#' 
#' Basic usage
#' $ conda list --export | awk -f list_export_to_yaml.awk
#' 
#' Omitting builds with 'no_builds'
#' $ conda list --export | awk -v no_builds=1 -f list_export_to_yaml.awk

mfansler

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

mfansler

name: kallisto-build
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - autoconf
  - automake
  - hdf5
  - make

mfansler

name: genewalk
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - pandas
  - networkx>=2.1
  - gensim
  - goatools

mfansler

library(tidyverse)

# values at which to evaluate
# this can be changed arbitrarily
x <- c(1,2,3) 

# evaluate y's for every condition and output a long format table
df <- expand.grid(coef=c(1,2), pow=c(1,2,3)) %>%
  group_by(coef, pow) %>%
  mutate(y=map2(coef, pow, ~ tibble(x=x, y=.x*x^.y))) %>%