moldach

I am attesting that this GitHub handle moldach is linked to the Tezos account tz1epnSBiaR334dL3wuX2TN9S52EJMGeSkXn for tzprofiles

sig:edsigtmnQtArWu3h1TuFqrh6g6bRJSM45w2Pxd4CXyExqx6Yaf4fLVqmnBSTa3YGkKiaWt7rBxUhVmz4vJphpzcCueq8ptmfPAk

moldach

Gene	Symbol	Gene_description	Chromosome	Start	End	NCBI	WormBase	WormBase_seq	GO	Human_GeneID	Human_GeneName	Identity	Human_Identity
WBGene00000001	aap-1	Phosphoinositide 3-kinase adapter subunit; Phosphoinositide kinase AdAPter subunit  [Source:UniProtKB/TrEMBL;Acc:G5EDP9]	I	5107833	5110183	172141	aap-1	Y110A7A.10	kinase activity	ENSG00000117461	PIK3R3	18.9655	21.4751
WBGene00000001	aap-1	Phosphoinositide 3-kinase adapter subunit; Phosphoinositide kinase AdAPter subunit  [Source:UniProtKB/TrEMBL;Acc:G5EDP9]	I	5107833	5110183	172141	aap-1	Y110A7A.10	phosphorylation	ENSG00000117461	PIK3R3	18.9655	21.4751
WBGene00000001	aap-1	Phosphoinositide 3-kinase adapter subunit; Phosphoinositide kinase AdAPter subunit  [Source:UniProtKB/TrEMBL;Acc:G5EDP9]	I	5107833	5110183	172141	aap-1	Y110A7A.10	protein kinase binding	ENSG00000117461	PIK3R3	18.9655	21.4751
WBGene00000001	aap-1	Phosphoinositide 3-kinase adapter subunit; Phosphoinositide kinase AdAPter subunit  [Source:UniProtKB/TrEMBL;Acc:G5EDP9]	I	5107833	5110183	172141	a

moldach

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 <<<<<<<<<<<<<<<<<<<<<<

moldach

moldach

 '''
    
    This is a snakemake for variant calling workflow
    
  
    -------------------
    # An example run of this workflow
    
    Usage:
    	snakemake --profile slurm --jobs 20 

moldach

/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
checking whether the C compiler works... yes

moldach

!#/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

moldach

# 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,

moldach

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

moldach

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

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