| from cm.services.apps import ApplicationService | |
| import logging | |
| log = logging.getLogger('cloudman') | |
| class BaseJobManager(ApplicationService): | |
| def __init__(self, app): | |
| super(BaseJobManager, self).__init__(app) |
| ... | |
| galaxy.queue_worker INFO 2015-05-06 16:33:13,705 Binding and starting galaxy control worker for main | |
| Starting server in PID 3058. | |
| serving on http://127.0.0.1:8080 | |
| galaxy.jobs.runners.drmaa DEBUG 2015-05-06 16:33:13,898 (114/115) state change: job finished, but failed | |
| galaxy.jobs.runners.slurm WARNING 2015-05-06 16:33:13,942 (114/115) Job not found, assuming job check exceeded MinJobAge and completing as successful | |
| galaxy.datatypes.metadata DEBUG 2015-05-06 16:33:14,202 setting metadata externally failed for HistoryDatasetAssociation 117: External set_meta() not called | |
| [bam_index_core] the alignment is not sorted (ERR030882.10002135): 3053935 > 3053755 in 25-th chr | |
| [bam_index_build2] fail to index the BAM file. | |
| *** Error in `python': double free or corruption (out): 0x00007faff008e9b0 *** |
| { | |
| "user": { | |
| "debug": true, | |
| "delay": 0.25, | |
| "error_color": "D02000", | |
| "gutter_theme": "Packages/SublimeLinter/gutter-themes/Blueberry/cross/Blueberry - cross.gutter-theme", | |
| "gutter_theme_excludes": [], | |
| "lint_mode": "save only", | |
| "linters": { | |
| "flake8": { |
| <% | |
| root = h.url_for( "/" ) | |
| app_root = root + "plugins/visualizations/popularity/static/" | |
| title = "Tool popularity derived from dataset '" + hda.name + "'" | |
| ## creating_job = hda.creating_job.id | |
| creating_job = trans.security.encode_id( hda.creating_job.id ) | |
| creating_job_id = hda.creating_job.id | |
| tool1 = hda.creating_job.tool_id | |
| # optionally bootstrap data from dprov |
| const gulp = require('gulp'); | |
| const del = require('del'); | |
| const typescript = require('gulp-typescript'); | |
| const tscConfig = require('./tsconfig.json'); | |
| // clean the contents of the distribution directory | |
| gulp.task('clean', function () { | |
| return del('dist/**/*'); | |
| }); |
| [defaults] | |
| allow_world_readable_tmpfiles=True | |
| callback_whitelist = profile_tasks |
| --- | |
| - 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 |
| 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') |
| import boto | |
| import boto.s3.connection | |
| from boto.ec2.regioninfo import RegionInfo | |
| # Provide access info for your cloud and your account | |
| A_KEY = "" | |
| S_KEY = "" | |
| region_name = 'Chameleon' | |
| region_endpoint = 'openstack.tacc.chameleoncloud.org' | |
| ec2_conn_path = "/services/Cloud" |
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