-
Create local repo and create/add/edit required files and dirs
egREADME.md,Dockerfile,.gitignore,.github/workflows/docker-image.yml -
On GitHub select "New repository" from the "+" menu and set name to match local repo.
Do not add any template files. -
Initialize up local repo and push to GitHub:
(assumes currently in local repo root dir)
mattgalbraith
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| tibble(x = seq(0, 15, by = 0.5), y = seq(0, 15, by = 0.5)) |> | |
| ggplot(aes(x, y)) + | |
| geom_point() + | |
| scale_y_continuous(breaks = \(x) seq(0, max(x), by = 1)) |
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| # Check length of reads | |
| zcat FASTQ_FILE.gz | head -n40 | paste - - - - | cut -f2,2 | awk '{print length}' | |
| # Check number and distribution of quality scores | |
| zcat FASTQ_FILE.gz | head -n400000 | paste - - - - | cut -f 4 | sed -e $'s/\(.\)/\\1\\\n/g' | sort | uniq -c |
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| # Ignore .DS_Store | |
| .DS_Store | |
| # Ignore R image files | |
| rdata/*RData | |
| ##################################### | |
| # From Github R .gitignore template # | |
| ##################################### | |
| # History files |
mattgalbraith
/ wget_CVATICA_download.txt
Last active
October 12, 2023 22:38
Download files from CAVATICA via text files with temporary (48hrs) file links
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| cat download_links.txt | xargs -P 1 wget --content-disposition --trust-server-names -nv -a wget_downloading.log |
mattgalbraith
/ temp_BAM_FASTQ_cleanup_and_transfer.sh
Created
February 17, 2023 04:36
Clean up temporary FASTQ and BAM files from BaSH_*seq v1.2 pipeline
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| # Run from inside analysis_dir | |
| echo "Original disk usage:" > temp_BAM_files_deleted.txt | |
| du -hs $PWD >> temp_BAM_files_deleted.txt | |
| echo "##########" >> temp_BAM_files_deleted.txt | |
| echo "Deletion of temporary BAM files:" >> temp_BAM_files_deleted.txt | |
| # Delete temp bam files | |
| for BAM in $(find $PWD/Sample_*/Alignments/ -name *mapped.no-rgid.bam); do echo $BAM >> temp_BAM_files_deleted.txt; rm $BAM; done | |
| for BAM in $(find $PWD/Sample_*/Alignments/ -name *mapped.rgid.bam); do echo $BAM >> temp_BAM_files_deleted.txt; rm $BAM; done |
mattgalbraith
/ gg_color_hue.R
Created
February 1, 2023 18:27
R function to get hex codes for standard ggplot colors
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| # get standard ggplot colors | |
| gg_color_hue <- function(n) { | |
| hues = seq(15, 375, length = n + 1) | |
| hcl(h = hues, l = 65, c = 100)[1:n] | |
| } |
mattgalbraith
/ obj_size.R
Created
February 1, 2023 18:25
R function to get object size in human-readable units
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| obj_size <- function(x) object.size(x) %>% print(units = "auto") |
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| mem_used <- function() lobstr::mem_used() %>% as.numeric() %>% R.utils::hsize() |
mattgalbraith
/ export_excel.R
Last active
February 1, 2023 18:37
R function to export tables in XLSX format
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| ## Excel export function | |
| export_excel <- function(named_list, filename = "") { | |
| wb <- openxlsx::createWorkbook() | |
| ## Loop through the list of split tables as well as their names | |
| ## and add each one as a sheet to the workbook | |
| Map(function(data, name){ | |
| openxlsx::addWorksheet(wb, name) | |
| openxlsx::writeData(wb, name, data) | |
| }, named_list, names(named_list)) | |
| ## Save workbook to working directory |
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