natefoo

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
        <plugin id="walltime" type="runner" load="galaxy.jobs.runners.walltime:WalltimeJobRunner" workers="4"/>
    </plugins>
    <handlers default="main">
        <handler id="main"/>
    </handlers>
    <destinations default="short">

natefoo

---
- hosts: localhost
  connection: local
  vars:
    build_id: gcc2014
    work_dir: /home/galaxy/nginx-build
    nginx_version: 1.4.7
    nginx_sha256: 23b8ff4a76817090678f91b0efbfcef59a93492f6612dc8370c44c1f1ce1b626
    nginx_upload_module_repo: https://github.com/vkholodkov/nginx-upload-module.git
    nginx_upload_module_branch: 2.2

natefoo

---
# vars

my_config:
  - section: foo
    options:
      - foo: bar
      - baz: quux

---

natefoo

---
- hosts: localhost
  connection: local
  vars:
    galaxy_config:
      "server:web0":
        host: 0.0.0.0
        port: 8080
      "server:web1":
        host: 0.0.0.0

natefoo

galaxy_mutable_configs:
  - src: "{{ galaxy_server_dir }}/migrated_tools_conf.xml.sample"
    dest: "{{ galaxy_config['app:main']['migrated_tools_config'] if galaxy_config is defined and 'app:main' in galaxy_config and 'migrated_tools_config' in galaxy_config['app:main'] else galaxy_config_default['app:main']['migrated_tools_config'] }}"

natefoo

(ansible)[nate@galaxy usegalaxy-playbook]$ pass ansible/vault/usegalaxy | ansible-playbook -i stage/inventory galaxy.yml --vault-password-file=/dev/stdin
Traceback (most recent call last):
  File "/home/ndc/ansible/bin/ansible-playbook", line 309, in <module>
    sys.exit(main(sys.argv[1:]))
  File "/home/ndc/ansible/bin/ansible-playbook", line 125, in main
    vault_pass = utils.read_vault_file(options.vault_password_file)
  File "/home/ndc/ansible/lib/python2.6/site-packages/ansible/utils/__init__.py", line 170, in read_vault_file
    if is_executable(this_path):
  File "/home/ndc/ansible/lib/python2.6/site-packages/ansible/utils/__init__.py", line 280, in is_executable
    return (stat.S_IXUSR & os.stat(path)[stat.ST_MODE]

natefoo

---
- hosts: all
  roles:
    - packages
    - role: nginx
      when: inventory_hostname in groups['webservers']
    - role: moin
      when: inventory_hostname in groups['wikiservers']

---

natefoo

% sacct -u g2main -L -s CA -S 2014-10-01 -E now -o 'jobname%-128' -X -n | cut -d_ -f1 | tr -d '^g' | (echo -n "select tool_id,count(tool_id) ct from job where id in("; while read jobid; do [[ $jobid =~ ^-?[0-9]+$ ]] && echo -n "$c$jobid"; c=','; done; echo ") and state='error' group by tool_id order by ct") | psql galaxy_main
                                              tool_id                                              | ct 
---------------------------------------------------------------------------------------------------+----
 toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0                      |  1
 toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0                             |  1
 toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1                  |  1
 Extract genomic DNA 1                                                                             |  1
 gff2bed1                                                             

natefoo

diff -r 3eda7cc3555c hmm/tool_dependencies.xml
--- a/hmm/tool_dependencies.xml	Mon Nov 12 14:52:05 2012 -0500
+++ b/hmm/tool_dependencies.xml	Wed Dec 03 15:47:48 2014 -0500
@@ -4,18 +4,6 @@
         <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
     <package name="R" version="2.15.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.0.tar.gz</action>

natefoo

nate@weyerbacher% python
Python 2.7.6 (default, Mar 22 2014, 22:59:56) 
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import os, tempfile
>>> f = tempfile.NamedTemporaryFile()
>>> f.name
'/tmp/tmptZ3yCX'
>>> os.rename(f.name, '/tmp/foo')
>>> f.write('foo\n')