Thanh Lee thanhleviet

NCBI blastp seems to have a bug where it reports different top hits when -max_target_seqs is changed. This is a serious problem because the first 20 hits (for example) should be the same whether -max_target_seqs 100 or -max_target_seqs 500 is used.

The bug is reproducible on the command line when searching NCBI's nr blast database (dated 25-Nov-2015) using NCBI 2.2.28+, 2.2.30+ and 2.2.31+.

At first I thought it was something to do with my local exe/blastdb, but the same problem is also apparent on the NCBI blastp web interface (as of 30-Nov-2015)

In this article, I will share some of my experience on installing NVIDIA driver and CUDA on Linux OS. Here I mainly use Ubuntu as example. Comments for CentOS/Fedora are also provided as much as I can.

Binding to C Libraries with Nim

libvirt + prometheus + grafana

KVM を libvirt でホストしていて、prometheus と grafana で観測したい場合。 exporter の実装は 3 種類みつかる。流儀が異なり、メトリクスが異なるので注意。

libvirt_exporter (Go)
- grafana json + prometheus recording rule
- prometheus の設定ファイルで recording rule を有効化します。
- job 名は libvirt_exporter

	library(twitteR)
	library(rlist)
	library(pipeR)
	library(stringi)

	# Authenticate with twitter
	# consumer/access keys and secrets for the twitter API must be defined elsewhere
	setup_twitter_oauth(consumer_key, consumer_secret, access_token, access_secret)

	# Get all my followers and followees

	#!/usr/bin/python

	import sys

	'''
	Just a simple tool that adds the line number at
	the end of each line
	'''

	with open(sys.argv[1]) as f_in, open(sys.argv[2], 'w') as f_out:

	#!/bin/bash
	# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
	#
	# Deinterleaves a FASTQ file of paired reads into two FASTQ
	# files specified on the command line. Optionally GZip compresses the output
	# FASTQ files using pigz if the 3rd command line argument is the word "compress"
	#
	# Can deinterleave 100 million paired reads (200 million total
	# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
	#

	If a handler log is full of messages like:

	Workflow step 1585 of invocation 554 delayed

	then probably a workflow invocation is stuck because a step was cancelled by a user. After verifying that this is the case, to stop the workflow invocation scheduling connect to the Galaxy database using psql and do the following:

	galaxy_db=> SELECT * FROM workflow_invocation WHERE id=554;
	id \| create_time \| update_time \| workflow_id \| history_id \| state \| scheduler \| handler \| uuid
	-----+----------------------------+----------------------------+-------------+------------+-------+-----------+----------+----------------------------------
	554 \| 2016-11-16 17:24:38.586902 \| 2016-11-16 17:26:34.555872 \| 201 \| 485 \| ready \| core \| handler1 \| 8d49678eac2111e697b90050569af9e3


	- name: Install Conda
	block:
	- name: Download Miniconda
	get_url:
	url: https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
	dest: /tmp/install-miniconda.sh
	checksum: md5:a946ea1d0c4a642ddf0c3a26a18bb16d
	mode: 0550
	- name: Create conda folder

Thanh Lee thanhleviet

Table of Contents

Binding to C Libraries with Nim

Table of Contents

libvirt + prometheus + grafana