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Enis Afgan afgane

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@afgane
afgane / Dockerfile_singleStage
Last active June 6, 2019 21:38
A version of the Dockerfile for building the minimal Galaxy image using a single stage build.
FROM ubuntu:18.04
# Init ARGs
ARG ROOT_DIR=/galaxy
ARG SERVER_DIR=$ROOT_DIR/server
# NOTE: the value of GALAXY_USER must be also hardcoded in COPY in final stage
ARG GALAXY_USER=galaxy
ARG DEBIAN_FRONTEND=noninteractive
# Install build dependencies + ansible
RUN set -xe; \
@afgane
afgane / enis42.sql
Created June 5, 2019 17:50
--
-- PostgreSQL database dump
--
-- Dumped from database version 10.6 (Debian 10.6-1.pgdg90+1)
-- Dumped by pg_dump version 10.6 (Debian 10.6-1.pgdg90+1)
SET statement_timeout = 0;
SET lock_timeout = 0;
SET idle_in_transaction_session_timeout = 0;
@afgane
afgane / galaxy.log
Created June 4, 2019 17:28
This file has been truncated, but you can view the full file.
*** Starting uWSGI 2.0.18 (64bit) on [Tue Jun 4 07:45:34 2019] ***
compiled with version: 4.8.2 20140120 (Red Hat 4.8.2-15) on 13 February 2019 12:48:51
os: Linux-4.4.0-1057-aws #66-Ubuntu SMP Thu May 3 12:49:47 UTC 2018
nodename: roiling-termite-galaxy-web-8f6bc47c6-mwm4q
machine: x86_64
clock source: unix
pcre jit disabled
detected number of CPU cores: 4
current working directory: /galaxy/server
detected binary path: /galaxy/server/.venv/bin/python2.7
@afgane
afgane / Galaxy CVMFS
Created May 20, 2019 21:32
Directory layout of the Galaxy CVMFS: data.galaxyproject.org
|-- byhand
| |-- AaegL1
| | |-- bowtie2_index
| | |-- bowtie_index
| | | `-- cs
| | |-- bwa_index
| | |-- picard_index
| | |-- sam_index
| | `-- seq
| |-- AgamP3
@afgane
afgane / dashboard.yml
Created May 15, 2019 13:39
# Copyright 2017 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
@afgane
afgane / dyndests.py
Created November 12, 2018 14:06
GVL instance setup for Pulsar bursting
# /mnt/galaxy/galaxy-app/lib/galaxy/jobs/rules/dyndests.py
from galaxy.jobs import JobDestination
import os
import multiprocessing
from galaxycloudrunner.server import get_next_server
# This rules file determines the number of local cpus and then sets the
# Slurm --ntasks parameter appropriately. The maximum and minimum cpus
# to use per job is listed below. These values can be altered to suit the
@afgane
afgane / Agenda.md
Last active August 14, 2018 15:47
Federated Galaxy calls

2018-08-14

  • CloudBridge 1.0 release
  • Galaxy download data tool PR #6853
  • GVL with Galaxy 18.05 testing

2018-08-08

@afgane
afgane / intro.py
Created August 2, 2016 19:18
A complete CloudBridge intro script
from cloudbridge.cloud.factory import CloudProviderFactory, ProviderList
# Add your cloud provider info, for example:
# config = {'aws_access_key': 'access key',
# 'aws_secret_key': 'secret key'}
# provider = CloudProviderFactory().create_provider(ProviderList.AWS, config)
# image_id = 'ami-2d39803a' # Ubuntu 14.04 (HVM)
# Create a key pair
kp = provider.security.key_pairs.create('CB-intro')
@afgane
afgane / playbook.yml
Created June 23, 2016 23:11
Setting up a server for CloudLaunch
---
- hosts: ansible-hosts
become: yes
become_user: root
tasks:
- name: Add Ansible PPA
apt_repository: repo={{ item }} update_cache=no
with_items:
- ppa:fkrull/deadsnakes
@afgane
afgane / README.md
Created June 23, 2016 16:00
An Ansible playbook for setting up a host to run Ansible itself.

Create an inventory file such called hosts with the following content (adjusting the IP address)

[ansible-hosts]
129.114.18.39 ansible_ssh_private_key_file=key_pair.pem ansible_ssh_user=ubuntu  # Ubuntu target

From an Ansible-enabled machine, download playbook.yml and run it with