raonyguimaraes

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

raonyguimaraes

#!/usr/bin/python
# -*- coding: utf-8 -*-

# gotoclass.py

import wx
import os
import csv

class FileConversion(wx.Frame):

raonyguimaraes

Traceback (most recent call last):
  File "/home/ubuntu/.local/bin/galaxy-tool-test", line 11, in <module>
    sys.exit(main())
  File "/home/ubuntu/.local/lib/python2.7/site-packages/galaxy/tools/verify/script.py", line 28, in main
    galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
  File "/home/ubuntu/.local/lib/python2.7/site-packages/galaxy/tools/verify/interactor.py", line 68, in __init__
    self.api_key = self.__get_user_key(kwds.get("api_key"), kwds.get("master_api_key"), test_user=kwds.get("test_user"))
  File "/home/ubuntu/.local/lib/python2.7/site-packages/galaxy/tools/verify/interactor.py", line 78, in __get_user_key
    test_user = self.ensure_user_with_email(test_user)
  File "/home/ubuntu/.local/lib/python2.7/site-packages/galaxy/tools/verify/interactor.py", line 498, in ensure_user_with_email

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#!/bin/bash
sudo pip install ansible
git clone https://github.com/ARTbio/GalaxyKickStart
cd GalaxyKickStart
git checkout 2018-gccbosc
ansible-galaxy install -r requirements_roles.yml -p roles --force
cat <<EOT >> group_vars/gccbosc18.yml
galaxy_root_dir: /srv/galaxy
galaxy_server_dir: "{{ galaxy_root_dir }}/server"
galaxy_venv_dir: "{{ galaxy_root_dir }}/venv"

raonyguimaraes

# Install bcbio

mkdir bcbio
cd bcbio
wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
mkdir data tooldir
python bcbio_nextgen_install.py data --tooldir=tooldir \
  --genomes GRCh37 --aligners bwa --aligners bowtie2
cd ../

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sudo apt install mysql-server
sudo apt-get install ubuntu-restricted-extras med-bio

#qt5
sudo apt install qt5-default
sudo apt-get install qtdeclarative5-dev qml-module-qtquick-controls
qttools5-dev libqt5x11extras5-dev qtbase5-dev

sudo apt-get install ubuntu-restricted-extras med-bio

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from subprocess import call, run
from multiprocessing import Pool

command = 'wget -r -l 1 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/'
run(command, shell=True)

path = '/storage3/1000genomes/ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502'

ind_file = open('{}/individuals.txt'.format(path))

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from subprocess import run
from multiprocessing import Pool

regions = ['1:1-50000000', '1:50000001-100000000', '1:100000001-150000000', '1:150000001-200000000', '1:200000001-250000000', '2:1-50000000', '2:50000001-100000000', '2:100000001-150000000', '2:150000001-200000000', '2:200000001-250000000', '3:1-50000000', '3:50000001-100000000', '3:100000001-150000000', '3:150000001-200000000', '4:1-50000000', '4:50000001-100000000', '4:100000001-150000000', '4:150000001-200000000', '5:1-50000000', '5:50000001-100000000', '5:100000001-150000000', '5:150000001-200000000', '6:1-50000000', '6:50000001-100000000', '6:100000001-150000000', '6:150000001-200000000', '7:1-50000000', '7:50000001-100000000', '7:100000001-150000000', '7:150000001-200000000', '8:1-50000000', '8:50000001-100000000', '8:100000001-150000000', '9:1-50000000', '9:50000001-100000000', '9:100000001-150000000', '10:1-50000000', '10:50000001-100000000', '10:100000001-150000000', '11:1-50000000', '11:50000001-100000000', '11:100000001-150000000', '12:1-

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raonyguimaraes

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