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
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
#!/usr/bin/python | |
# -*- coding: utf-8 -*- | |
# gotoclass.py | |
import wx | |
import os | |
import csv | |
class FileConversion(wx.Frame): |
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 |
#!/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" |
# 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 ../ |
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 |
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)) |
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- |
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