Leah Kemp leahkemp
leahkemp
/ add_large_files_to_git_ignore.sh
Created
August 17, 2021 00:57
Add all files greater than a certain size to the .gitinore file
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| # Note. 2G is the maximum file size to be pushed to github with Git Large File Storage | |
| echo "# Files over 2G" >> .gitignore | |
| find * -size +2G -type f -print >> .gitignore |
leahkemp
/ get_num_reads_per_fastq.sh
Created
August 17, 2021 00:48
Generate a csv file with number of reads in each fastq in a directory of fastq files
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| #!/bin/bash | |
| ##### INFO ##### | |
| # this script generates a csv file with the number of reads in each fastq file in a directory of | |
| # fastq files | |
| ##### USER PARAMETERS ##### | |
| # Set the fastq directory | |
| fastq_dir="/home/user/fastq" |
leahkemp
/ unique_chromosomes_vcf
Created
July 27, 2020 00:32
Return unique chromosome values in vcf
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| zgrep -v "#" file.gz | awk '{print $1}' | uniq |
leahkemp
/ white_spaces_to_tab_spaces.sh
Last active
July 20, 2020 22:06
Convert white spaces to tab spaces
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| # Code by Miles Benton | |
| # An example pedigree file | |
| # Using cat | |
| cat pedigree.ped | tr ' ' '\t' | |
| # Using sed | |
| sed -i 's/ /\t/g' pedigree.ped |
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| nvidia-smi | |
| nvtop |
leahkemp
/ ftp_directory_download.sh
Last active
July 22, 2020 21:43
Download everything from an ftp directory in parallel
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| # Code by Miles Benton | |
| # An example for downloading everything from the GATK resource bundle (b37) | |
| curl -l ftp://ftp.broadinstitute.org/bundle/b37/ --user gsapubftp-anonymous | \ | |
| sed -e 's/^/ftp:\/\/ftp.broadinstitute.org\/bundle\/b37\//' | \ | |
| parallel -j15 wget --user=gsapubftp-anonymous --password="" | |
| curl -l ftp://ftp.broadinstitute.org/bundle/b37/ --user gsapubftp-anonymous | sed -e 's/^/ftp:\/\/ftp.broadinstitute.org\/bundle\/b37\//' > ftp-files.txt \ | |
| cat ftp-files.txt | parallel -j5 wget --user=gsapubftp-anonymous --password="" |
leahkemp
/ leaflet_transform.R
Last active
February 25, 2020 22:19
Transform a Shape file to correctly work in Leaflet
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| "shape <- shapefile("../data.shp") %>% | |
| st_as_sf()" | |
| shape_transformed <- shape %>% as_Spatial() %>% spTransform(CRS("+proj=longlat +datum=WGS84 +no_defs +lon_wrap=180")) |