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@ckandoth
ckandoth / ensembl_vep_102_with_offline_cache.md
Last active November 7, 2023 14:32
Install Ensembl's VEP v102 with local cache for running offline

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

Instead of the official instructions, we will use conda to install VEP and its dependencies. If you don't already have conda, install it into $HOME/miniconda3 as follows:

curl -sL https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh -o /tmp/miniconda.sh
sh /tmp/miniconda.sh -bfp $HOME/miniconda3

Add the conda bin folder into your $PATH so that all installed tools are accessible via command-line. You can also add this to your ~/.bashrc

@knmkr
knmkr / tabix-s3-example.md
Last active February 20, 2021 08:37
tabix s3 example

Tabix command of htslib can query a locus to a remote s3 file using s3:// protocol.

$ aws s3 ls s3://your_bucket/
vcf.gz
vcf.gz.tbi

$ tabix -l s3://your_bucket/vcf.gz
chr1
chr2
@mvdbeek
mvdbeek / mysql_migration.txt
Created June 25, 2018 23:26
mysql database migration errors on fresh mysql database
galaxy.queue_worker INFO 2018-06-25 16:18:23,098 [p:48241,w:0,m:0] [MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+mysql+mysqldb://mvandenb:********@localhost/galaxy
galaxy.model.migrate.check INFO 2018-06-25 16:18:23,268 [p:48241,w:0,m:0] [MainThread] No database, initializing
galaxy.model.migrate.check INFO 2018-06-25 16:18:23,309 [p:48241,w:0,m:0] [MainThread] Migrating 0 -> 1...
galaxy.model.migrate.check INFO 2018-06-25 16:18:24,589 [p:48241,w:0,m:0] [MainThread]
galaxy.model.migrate.check INFO 2018-06-25 16:18:24,589 [p:48241,w:0,m:0] [MainThread] Migrating 1 -> 2...
galaxy.model.migrate.check INFO 2018-06-25 16:18:24,745 [p:48241,w:0,m:0] [MainThread]
galaxy.model.migrate.check INFO 2018-06-25 16:18:24,745 [p:48241,w:0,m:0] [MainThread] Migrating 2 -> 3...
galaxy.model.migrate.check INFO 2018-06-25 16:18:27,040 [p:48241,w:0,m:0] [MainThread]
galaxy.model.migrate.check INFO 2018-06-25 16:18:27,040 [p:48241,w:0,m:0] [MainThread] Migrating 3 -> 4...
/Users/mvandenb/src/galaxy/.venv/lib/py
@alexandari
alexandari / basset_sfc_setup.py
Created June 5, 2017 18:33
SFC Layers Example: Basset Model with SFC Layer Setup
#install keras from https://github.com/kundajelab/keras/tree/keras_1
from __future__ import print_function
import keras
import numpy as np
np.random.seed(1)
#build a model
model = keras.models.Sequential()
model.add(keras.layers.convolutional.Convolution1D(input_shape=(1000,4),
nb_filter=300,
@kapcom01
kapcom01 / nextcloud-snap-backup.sh
Created February 21, 2017 15:02
#! /bin/bash
user=manolis
backups=/home/manolis/backups
if [[ $EUID > 0 ]]
then echo "Please run as root"
exit
fi
@yossorion
yossorion / what-i-wish-id-known-about-equity-before-joining-a-unicorn.md
Last active June 25, 2024 07:29
What I Wish I'd Known About Equity Before Joining A Unicorn

What I Wish I'd Known About Equity Before Joining A Unicorn

Disclaimer: This piece is written anonymously. The names of a few particular companies are mentioned, but as common examples only.

This is a short write-up on things that I wish I'd known and considered before joining a private company (aka startup, aka unicorn in some cases). I'm not trying to make the case that you should never join a private company, but the power imbalance between founder and employee is extreme, and that potential candidates would

@rondy
rondy / Effective_Engineer.md
Last active June 28, 2024 07:44

FWIW: I (@rondy) am not the creator of the content shared here, which is an excerpt from Edmond Lau's book. I simply copied and pasted it from another location and saved it as a personal note, before it gained popularity on news.ycombinator.com. Unfortunately, I cannot recall the exact origin of the original source, nor was I able to find the author's name, so I am can't provide the appropriate credits.

Effective Engineer - Notes

What's an Effective Engineer?

@Jabolcnik
Jabolcnik / README.md
Last active November 17, 2022 22:27
wkhtmltopdf centos 7 headless with xvfb

wkhtmltopdf centos 7 headless with xvfb

Install and run standalone Xvfb

yum install xorg-x11-server-Xvfb
yum install xorg-x11-fonts-Type1 xorg-x11-fonts-75dpi
wget http://download.gna.org/wkhtmltopdf/0.12/0.12.2.1/wkhtmltox-0.12.2.1_linux-centos7-amd64.rpm
rpm -ivh wkhtmltox-0.12.2.1_linux-centos7-amd64.rpm
@acamino
acamino / README.md
Last active June 17, 2024 03:03
Shortcuts to Improve Your Bash & Zsh Productivity

Shortcut — Action

  • CTRL + A — Move to the beginning of the line
  • CTRL + E — Move to the end of the line
  • CTRL + [left arrow] — Move one word backward (on some systems this is ALT + B)
  • CTRL + [right arrow] — Move one word forward (on some systems this is ALT + F)
  • CTRL + U — (bash) Clear the characters on the line before the current cursor position
  • CTRL + U —(zsh) If you're using the zsh, this will clear the entire line
  • CTRL + K — Clear the characters on the line after the current cursor position
  • ESC + [backspace] — Delete the word in front of the cursor
@eirikb
eirikb / clicktest.md
Last active April 9, 2021 16:49
Automated click testing in bash

About

This is a bash script, as an example, on how to do click-testing GUI based on finding components based on how they look.

Dependencies