Matthew J. Oldach moldach

## fastqc_wrapper_nohup.out
Workflow defines that rule get_vep_cache is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
Creating conda environment https:/github.com/snakemake/snakemake-wrappers/raw/0.66.0/bio/vep/plugins/environment.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /tmp/tmpisqd78u6.yaml:
Solving environment: ...working... failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

## survivor_comparison_matrix.tsv

          
            Breakdancer
            CNVnator
            DeepVariant
            Delly
            GRIDSS
            Lumpy
            Manta
            MindTheGap
            NGSep
            Pindel
            Tardis

            
              0
              0
              0
              0
              1
              0
              1
              0
              0
              0
              0

            
              0
              0
              0
              0
              1
              0
              1
              0
              0
              0
              0

            
              0
              0
              1
              0
              1
              0
              0
              0
              0
              0
              0

            
              0
              0
              0
              1
              0
              1
              1
              0
              0
              0
              1

            
              0
              0
              0
              1
              0
              1
              1
              0
              0
              0
              1

            
              0
              0
              0
              0
              1
              0
              1
              0
              0
              0
              0

            
              0
              0
              0
              1
              0
              1
              1
              0
              0
              0
              1

            
              1
              0
              0
              0
              1
              0
              0
              0
              1
              0
              0

            
              0
              0
              0
              1
              0
              0
              1
              0
              0
              0
              0

## Snakefile
 '''

    This is a snakemake for variant calling workflow


    -------------------
    # An example run of this workflow

    Usage:
    	snakemake --profile slurm --jobs 20

## pyenv_3.5.0_ubuntu-20.04.log
/tmp/python-build.20200520134504.60362 ~/projects/data/celegans
/tmp/python-build.20200520134504.60362/Python-3.5.0 /tmp/python-build.20200520134504.60362 ~/projects/data/celegans
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for --enable-universalsdk... no
checking for --with-universal-archs... no
checking MACHDEP... linux
checking for --without-gcc... no
checking for gcc... gcc

## r_ubuntu.sh
!#/bin/bash

set -o nounset # To exit when your script tries to use undeclared variables.
set -o xtrace # To trace what gets exectued (debugging).
set -e # Abort script at first error, when a command exits with non-zero status (except in until or while loops, if-tests, list constructs)
set -o pipefail # Causes a pipeline to return the exit status of the last command in the pipe that returned a non-zero return value.

# Install multiple versions of python
# https://github.com/pyenv/pyenv
# https://github.com/pyenv/pyenv/wiki#suggested-build-environment

## gist:d184be424098e69f2dde3599b6cba83c
# remotes::install_github("wilkelab/ggtext")

library(tibble)
library(ggplot2)
library(dplyr)

data <- tribble(
  ~bactname, ~OTUname, ~name, ~value,
  "Staphylococcaceae", "OTU1", "Staphylococcaceae (OTU1)", -0.5,
  "Moraxella", "OTU2", "Moraxella (OTU2)", 0.5,

## qs package for saving ggplot objects
library(bench)
library(qs)
library(sf)
library(cowplot)

# load ggplot
download.file("https://www.dropbox.com/s/ao0827vayr5u3vx/hawaii_agriculture_100m_basemap.rds?raw=1" , "hawaii_agriculture_100m_basemap.rds")
hawaii <- readRDS("hawaii_agriculture_100m_basemap.rds")

# bench mark saving

## import_QC_Koh
---
title: "Import and QC of Koh data set (SRP073808)"
output: html_document
editor_options:
  chunk_output_type: console
---

```{r load-packages}
suppressPackageStartupMessages({
  library(MultiAssayExperiment)

## gist:552cc704ced328a0120394271404779f
### This method works for Switzerland and The USA (shown here, at the top) but not Hawaii (shown at the bottom)
library(sf)
library(raster)
library(dplyr)
library(ggplot2)

## USA
# download shapefile: https://catalog.data.gov/dataset/tiger-line-shapefile-2017-nation-u-s-current-state-and-equivalent-national
usa_geo <- read_sf("data/shapefiles/usa/tl_2017_us_state.shp")

## ez-extract

# Extracting various compression files made easy
extract() {
  if [ -f $1 ] ; then
      case $1 in
          *.tar.bz2)   tar xvjf $1    ;;
          *.tar.gz)    tar xvzf $1    ;;
          *.bz2)       bunzip2 $1     ;;
          *.rar)       rar x $1       ;;
          *.gz)        gunzip $1      ;;
	Workflow defines that rule get_vep_cache is eligible for caching between workflows (use the --cache argument to enable this).
	Building DAG of jobs...
	Creating conda environment https:/github.com/snakemake/snakemake-wrappers/raw/0.66.0/bio/vep/plugins/environment.yaml...
	Downloading and installing remote packages.
	CreateCondaEnvironmentException:
	Could not create conda environment from /tmp/tmpisqd78u6.yaml:
	Solving environment: ...working... failed

	# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Breakdancer	CNVnator	DeepVariant	Delly	GRIDSS	Lumpy	Manta	MindTheGap	NGSep	Pindel	Tardis
0	0	0	0	1	0	1	0	0	0	0
0	0	0	0	1	0	1	0	0	0	0
0	0	1	0	1	0	0	0	0	0	0
0	0	0	1	0	1	1	0	0	0	1
0	0	0	1	0	1	1	0	0	0	1
0	0	0	0	1	0	1	0	0	0	0
0	0	0	1	0	1	1	0	0	0	1
1	0	0	0	1	0	0	0	1	0	0
0	0	0	1	0	0	1	0	0	0	0
	'''

	This is a snakemake for variant calling workflow


	-------------------
	# An example run of this workflow

	Usage:
	snakemake --profile slurm --jobs 20
	/tmp/python-build.20200520134504.60362 ~/projects/data/celegans
	/tmp/python-build.20200520134504.60362/Python-3.5.0 /tmp/python-build.20200520134504.60362 ~/projects/data/celegans
	checking build system type... x86_64-unknown-linux-gnu
	checking host system type... x86_64-unknown-linux-gnu
	checking for --enable-universalsdk... no
	checking for --with-universal-archs... no
	checking MACHDEP... linux
	checking for --without-gcc... no
	checking for gcc... gcc
	!#/bin/bash

	set -o nounset # To exit when your script tries to use undeclared variables.
	set -o xtrace # To trace what gets exectued (debugging).
	set -e # Abort script at first error, when a command exits with non-zero status (except in until or while loops, if-tests, list constructs)
	set -o pipefail # Causes a pipeline to return the exit status of the last command in the pipe that returned a non-zero return value.

	# Install multiple versions of python
	# https://github.com/pyenv/pyenv
	# https://github.com/pyenv/pyenv/wiki#suggested-build-environment
	# remotes::install_github("wilkelab/ggtext")

	library(tibble)
	library(ggplot2)
	library(dplyr)

	data <- tribble(
	~bactname, ~OTUname, ~name, ~value,
	"Staphylococcaceae", "OTU1", "Staphylococcaceae (OTU1)", -0.5,
	"Moraxella", "OTU2", "Moraxella (OTU2)", 0.5,
	library(bench)
	library(qs)
	library(sf)
	library(cowplot)

	# load ggplot
	download.file("https://www.dropbox.com/s/ao0827vayr5u3vx/hawaii_agriculture_100m_basemap.rds?raw=1" , "hawaii_agriculture_100m_basemap.rds")
	hawaii <- readRDS("hawaii_agriculture_100m_basemap.rds")

	# bench mark saving
	---
	title: "Import and QC of Koh data set (SRP073808)"
	output: html_document
	editor_options:
	chunk_output_type: console
	---

	```{r load-packages}
	suppressPackageStartupMessages({
	library(MultiAssayExperiment)
	### This method works for Switzerland and The USA (shown here, at the top) but not Hawaii (shown at the bottom)
	library(sf)
	library(raster)
	library(dplyr)
	library(ggplot2)

	## USA
	# download shapefile: https://catalog.data.gov/dataset/tiger-line-shapefile-2017-nation-u-s-current-state-and-equivalent-national
	usa_geo <- read_sf("data/shapefiles/usa/tl_2017_us_state.shp")

	# Extracting various compression files made easy
	extract() {
	if [ -f $1 ] ; then
	case $1 in
	*.tar.bz2) tar xvjf $1 ;;
	*.tar.gz) tar xvzf $1 ;;
	*.bz2) bunzip2 $1 ;;
	*.rar) rar x $1 ;;
	*.gz) gunzip $1 ;;