Philipp Bayer philippbayer

How to Limit CPU and Memory Usage With Cgroups on Debian/Ubuntu

Cgroups is a flexible Linux kernel feature to limit, police and account resources usage. A cgroup is a set of tasks for a subsystems, that is typically a resource controller.

A file system of type cgroup is mounted and all operations are run over it.

Installation

The installation can be done using any of libcgroup, cgmanager or systemd.

Goal

To create UniRef90 protein databases for NCBI blast and Diamond Blast
To create a tab delimited taxid mapping file with two columns : sequenceID\tNCBITaxonID

Steps:

Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)

	#Usage: conda-find.sh my-lost-package my-version

	conda info --envs \|
	grep -v "#" \|
	sed 's/\s\+/\t/' \|
	cut -f2 \|
	sed '/^$/d' \|
	sed 's/^\*\s\+//' \|
	while read line; do
	conda list -p $line \|

	import streamlit as st
	import io
	import contextlib
	import sys
	import re
	import threading


	class _Redirect:
	class IOStuff(io.StringIO):

	# in zenodo ui create a deposition. get the id

	curl -H "Accept: application/json" -H "Authorization: Bearer $TOKEN" "https://www.zenodo.org/api/deposit/depositions/$DEPOSITION"
	# get the bucket id from above

	curl --progress-bar -o /dev/null --upload-file ./$FILE https://www.zenodo.org/api/files/$BUCKET/$FILE?access_token=$TOKEN

	*bcftools filter
	*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
	qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

	*printing out info for only 2 samples:
	bcftools view -s NA20818,NA20819 filename.vcf.gz

	*printing stats only for variants passing the filter:
	bcftools view -f PASS filename.vcf.gz

	#!/bin/bash
	mkdir /tmp/adodefont
	cd /tmp/adodefont
	mkdir -p ~/.fonts

	wget https://github.com/adobe-fonts/source-code-pro/archive/2.030R-ro/1.050R-it.zip
	unzip 1.050R-it.zip
	cp source-code-pro-2.030R-ro-1.050R-it/OTF/*.otf ~/.fonts/

	wget https://github.com/adobe-fonts/source-serif-pro/archive/2.000R.zip

	# Create empty branch.
	git checkout --orphan review
	git rm -rf .
	git commit --allow-empty -m "Create empty branch"
	git push --set-upstream origin review

	# Create `project` branch from `master` current state.
	git checkout -b project
	git merge master --allow-unrelated-histories
	git push --set-upstream origin project

	#!/usr/bin/env perl


	=head1 [progam_name]

	description:
	- converts tped files to hapmap files.


	=head2 usage