Nate Coraor natefoo
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| Fetched 1,586 MB in 1min 40s (15.8 MB/s) | |
| texlive-base:amd64 conflicts with texlive-binaries:amd64 | |
| texlive-base:amd64 conflicts with texlive-binaries:amd64 | |
| texlive-base:amd64 conflicts with texlive-extra-utils:amd64 | |
| texlive-base:amd64 conflicts with texlive-font-utils:amd64 | |
| texlive-base:amd64 conflicts with texlive-binaries:amd64 | |
| texlive-base:amd64 conflicts with texlive-extra-utils:amd64 | |
| texlive-base:amd64 conflicts with texlive-font-utils:amd64 | |
| texlive-base:amd64 conflicts with texlive-fonts-extra:amd64 | |
| texlive-base:amd64 conflicts with texlive-binaries:amd64 |
natefoo
/ job_conf.xml
Last active
August 29, 2015 14:02
A fake job runner for testing the walltime resubmission feature committed in https://bitbucket.org/galaxy/galaxy-central/commits/7b209e06ddb944e953d340754439f4e3e5dc339d
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| <?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"> |
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| --- | |
| - 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
/ gist:18492a1f9dea787cd639
Created
August 19, 2014 19:22
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| --- | |
| # vars | |
| my_config: | |
| - section: foo | |
| options: | |
| - foo: bar | |
| - baz: quux | |
| --- |
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| --- | |
| - hosts: localhost | |
| connection: local | |
| vars: | |
| galaxy_config: | |
| "server:web0": | |
| host: 0.0.0.0 | |
| port: 8080 | |
| "server:web1": | |
| host: 0.0.0.0 |
natefoo
/ gist:dad269d55b8f533dc390
Created
August 27, 2014 18:03
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| 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
/ gist:357521f8da3774e465d6
Created
September 10, 2014 03:16
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| (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
/ gist:55f08e694379fd3fa3e7
Last active
August 29, 2015 14:07
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| --- | |
| - hosts: all | |
| roles: | |
| - packages | |
| - role: nginx | |
| when: inventory_hostname in groups['webservers'] | |
| - role: moin | |
| when: inventory_hostname in groups['wikiservers'] | |
| --- |
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| % 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
/ gist:732e233122ef7b8041e4
Created
December 3, 2014 20:48
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| 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> |
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