Matthew J. Oldach moldach
moldach
/ ez-extract
Created
September 21, 2017 19:38
Function to easily uncompress a variety of formats in Linux - add this to .bashrc. then run it on file (e.g. extract file.zip)
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| # 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 ;; |
moldach
/ gist:552cc704ced328a0120394271404779f
Created
October 2, 2019 17:42
Shapefiles and Raster of Relief do not match for Hawaii
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| ### 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") |
moldach
/ import_QC_Koh
Last active
September 14, 2021 22:34
Troubleshooting QC for scRNAseq_clustering_comparison
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| --- | |
| title: "Import and QC of Koh data set (SRP073808)" | |
| output: html_document | |
| editor_options: | |
| chunk_output_type: console | |
| --- | |
| ```{r load-packages} | |
| suppressPackageStartupMessages({ | |
| library(MultiAssayExperiment) |
moldach
/ qs package for saving ggplot objects
Last active
October 29, 2019 19:12
Troubleshooting bench::mark with qs::qread()
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| 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
/ gist:d184be424098e69f2dde3599b6cba83c
Created
February 5, 2020 18:21
ggtext troubleshooting
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| # 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
/ r_ubuntu.sh
Last active
August 7, 2024 10:07
— forked from luispuerto/r_ubuntu.sh
Install R and RStudio on Ubuntu 19.10 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location - /usr/local/lib/R/site-packages - is writable .
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| !#/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
/ pyenv_3.5.0_ubuntu-20.04.log
Created
May 20, 2020 19:48
pyenv install 3.5.0 failing for Ubuntu 20.04 LTS
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| /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 |
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| ''' | |
| This is a snakemake for variant calling workflow | |
| ------------------- | |
| # An example run of this workflow | |
| Usage: | |
| snakemake --profile slurm --jobs 20 |
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| 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 |
moldach
/ fastqc_wrapper_nohup.out
Created
September 22, 2020 23:01
Error log from snakemake fastqc wrapper when using --use-singularity and --use-conda on HPC
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| 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 <<<<<<<<<<<<<<<<<<<<<< |
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