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)
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ### 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| 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()
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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
May 6, 2020 15:13
— 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 .
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| !#/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
This file has been truncated, but you can view the full file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ''' | |
| This is a snakemake for variant calling workflow | |
| ------------------- | |
| # An example run of this workflow | |
| Usage: | |
| snakemake --profile slurm --jobs 20 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 <<<<<<<<<<<<<<<<<<<<<< |
OlderNewer