Galaxy Release Schedule
3 releases per year: January, May and September
Install Galaxy using Ansible
sudo pip install ansible
git clone https://github.com/ARTbio/GalaxyKickStart
git checkout 2018-gccbosc
ansible-galaxy install -r requirements_roles.yml -p roles –force
$ sudo su galaxy $ vi /srv/galaxy/config/galaxy.yml # Add the following line under galaxy: section admin_users: email@example.com $ exit # change back to ubuntu user $ sudo supervisorctl restart galaxy:
|09:00||Welcome and introduction||Slides||(Č)|
|09:15||Deployment and platform options||Slides||(Č)|
|9:30||Using Ansible to deploy Galaxy||Slides, Exercise||(E)(G)|
|10:20||Extending installation||Slides, Exercise||(G)|
|10:40||Defining and importing genomes, Data Managers||Slides, Exercise||(E)|
|11:15||Web Servers nginx/Apache||Slides||(M)(N)|
|11:30||Close Morning Session|
Galaxy admin -> local data: Create DBKey and Reference Genome – fetching
Install dbkey from saccer2 data_manager_fetch_genome_dbkeys_all_fasta
Install BWA data_manager_bwa_mem_index_builder
Admin -> create bwa index
ubuntu@2018-gcc-training-0:~⟫ sudo vim /srv/galaxy/config/galaxy.yml
#nginx_x_accel_redirect_base: False and change it to
nginx_x_accel_redirect_base: /_x_accel_redirect. Remember, this file is owned by the galaxy user so be sure to use
sudo -u galaxy when editing it.
sudo supervisorctl restart nginx galaxy:
Google’s PageSpeed Tools can identify any compression or caching improvements you can make.
If configuring SSL (out of scope for this training), out-of-the-box SSL settings are often insecure!
$ planemo test –no-container –engine toil seqtk_seq.cwl
#this will open the browser
Correspond to job runner plugins in lib/galaxy/jobs/runners
- Slurm (DRMAA subclass)
- DRMAA: SGE, PBS Pro, LSF, Torque
- Torque: Using the
- Pulsar: Galaxy’s own remote job management system
- Command Line Interface (CLI) via SSH
Need a shared file system, nfs, ceph and etc.
Exception is Pulsar!
sudo cat job_conf.xml.sample_basic <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <destinations> <destination id="local" runner="local"/> </destinations> </job_conf>
--- tools: multi: rules: - rule_type: file_size lower_bound: 16 upper_bound: Infinity destination: slurm-2c default_destination: slurm_cluster default_destination: local_no_container verbose: True
I think that the time has come to start talking seriously about bringing async functionality into Django itself, and so I have been working on a draft “roadmap” for what I think this might look like. I’ve run this past a few people – some of who were Django core members, and some who weren’t – but I’m now posting it up for public feedback (see the end for where to discuss this).
Machine learning offers a fantastically powerful toolkit for building complex systems quickly. This paper argues that it is dangerous to think of these quick wins as coming for free. Using the framework of technical debt, we note that it is remarkably easy to incur massive ongoing maintenance costs at the system level when applying machine learning. The goal of this paper is highlight several machine learning specific risk factors and design patterns to be avoided or refactored where possible. These include boundary erosion, entanglement, hidden feedback loops, undeclared consumers, data dependencies, changes in the external world, and a variety of system-level anti-patterns.
Machine Learning: The High Interest Credit Card of Technical Debt
Biology needs revolution. All my adult life, I have been lost with admirationfor the achievements in molecular biology and genetics, and I have come toknow many of the main proponents. Yet there is an alternative aspect: instudying the minutiae, we have lost sight of the whole cell as organism.Living cells within the body are modelled in this paper as coordinated butessentially autonomous entities. We shall see how independent cells innature have remarkable abilities to make decisions and take constructiveaction, which correlate with the definitions of intelligence.
An influential committee of the European Parliament is due to vote this month on changes to copyright regulations in the European Union, but the latest drafts of the rules have triggered a wave of criticism from open-science advocates. They say that the proposals will stifle research and scholarly communication.
It’s been a while since we last published a status update about React Native.
At Facebook, we’re using React Native more than ever and for many important projects. One of our most popular products is Marketplace, one of the top-level tabs in our app which is used by 800 million people each month. Since its creation in 2015, all of Marketplace has been built with React Native, including over a hundred full-screen views throughout different parts of the app.
We’re also using React Native for many new parts of the app. If you watched the F8 keynote last month, you’ll recognize Blood Donations, Crisis Response, Privacy Shortcuts, and Wellness Checks – all recent features built with React Native. And projects outside the main Facebook app are using React Native too. The new Oculus Go VR headset includes a companion mobile app that is fully built with React Native, not to mention React VR powering many experiences in the headset itself.
State of React Native 2018
Source: The Cyberpunk Sensibility
Prediction of the FIFA World Cup 2018 – A random forest approach with an emphasis on estimated team ability parameters