Matt Cannon MVesuviusC

MVesuviusC / R_package_install_fail.txt

Last active October 28, 2025 19:16

Error installing R packages on Franklin cluster

	install.packages("ggpubr")
	.
	.
	.
	.
	checking for suffix of object files... o
	checking whether the compiler supports GNU C++... yes
	checking whether g++ -std=gnu++14 accepts -g... yes
	checking for g++ -std=gnu++14 option to enable C++11 features... none needed
	checking how to run the C++ preprocessor... g++ -std=gnu++14 -E

MVesuviusC / ggvenn_fix

Created January 30, 2023 21:22

Fix ggvenn labels getting cut off

	venn_plot <- ggvenn::ggvenn(list_of_four_vectors)

	venn_plot$layers[[3]]$data$x <- c(-1, -0.8, 0.8, 1)

MVesuviusC / maint_time.txt

Last active October 23, 2023 15:03

get time till next maintenance on the HPC

	get_maint_time () {
	maint_start=$(scontrol show -u root reservation \
	\| perl -pe 's/\n/#/g' \
	\| perl -pe 's/#ReservationName=/\n/g' \
	\| grep MAINT \
	\| perl -ne '/.+StartTime=(.+)\sEndTime/; print $1;')
	difftime=$(($(date +%s -d "$maint_start") - $(date +%s) - 1000))
	req_len=$(date -d "@$difftime" "+$(($difftime/86400))-%H:%M:%S")
	echo $req_len
	}

MVesuviusC / find_chmod.txt

Created December 13, 2022 14:39

Find by user and permissions and chmod

	# find and chmod files that aren't 444 in a couple directories
	for directory in BCLs FASTQs Counts
	do
	find \
	/home/gdrobertslab/lab/${directory} \
	-user mvc002 \
	-type f \
	-not -perm 444 \
	\| xargs \
	-d '\n' \

MVesuviusC / id_illumina.txt

Created December 2, 2022 20:52

ID illumina instrument

MVesuviusC / R_on_GPU.txt

Last active September 30, 2022 16:33

running R on a GPU node

	Instructions taken from: https://clint.id.au/?p=1900

	srun -c 4 --gres=gpu --account=gdrobertslab --x11 --pty bash

	echo "NVBLAS_LOGFILE nvblas.log
	NVBLAS_CPU_BLAS_LIB /usr/local/cuda-11.6/lib64/libnvblas.so
	NVBLAS_GPU_LIST ALL" > ~/nvblas.conf

	module load CUDA/11.5.0

MVesuviusC / scron_jobs.txt

Last active June 12, 2023 12:27

scron jobs

	# List scron jobs
	scrontab -l

	#Edit scron job
	scrontab -e

	# If scrontab get disabled
	scrontab -e
	# Delete #DISABLED.... up until $SCRON

MVesuviusC / rstudio_sing.txt

Created April 19, 2022 13:22

rstudio server using singularity

	singularity rstudio
	modified from: https://www.rocker-project.org/use/singularity/


	#!/bin/bash
	#SBATCH --time=3-00:00:00
	#SBATCH --signal=USR2
	#SBATCH --ntasks=1

	module purge

MVesuviusC / xargs.txt

Created April 19, 2022 13:21

xargs bits

	samtools view -H yourFile.bam \| \
	grep "\@SQ" \| \
	sed 's/^.*SN://g' \| \
	cut -f 1 \| \
	xargs -I {} \
	-n 1 \
	-P 24 \
	sh -c "samtools mpileup -BQ0 -d 100000 -uf yourGenome.fa -r {} yourFile.bam \| bcftools view -vcg - > tmp.{}.vcf"

MVesuviusC / dnanexus_app_build.txt

Created April 19, 2022 13:20

DNAnexus app building

	DNAnexus app building

	source ~/virtualEnvs/dnanexus/bin/activate
	dx login # login to server, choose which project to attach to
	dx build # build app from the json and associated file(s)
	deactivate

	samtools view -H yourFile.bam \| \
	grep "\@SQ" \| \
	sed 's/^.*SN://g' \| \
	cut -f 1 \| \
	xargs -I {} \
	-n 1 \
	-P 24 \
	sh -c "samtools mpileup -BQ0 -d 100000 -uf yourGenome.fa -r {} yourFile.bam \| bcftools view -vcg - > tmp.{}.vcf"