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galaxy

Command Description
galaxy amqp-test Test a given AMQP URL for connectivity
galaxy cleanup Cleanup histories/hdas/etc for past N days (default=30)
galaxy cleanup-jwd (NEW) Cleanup job working directories
galaxy decode Decode an encoded ID
galaxy encode Encode an ID
galaxy fav-tools Favourite tools in Galaxy DB
galaxy fix-conda-env Fix broken conda environments
galaxy ie-list List GIEs
galaxy ie-show Report on a GIE [HTCondor Only!]
galaxy migrate-tool-install-from-sqlite Converts SQLite version into normal potsgres toolshed repository tables
galaxy migrate-tool-install-to-sqlite Converts normal potsgres toolshed repository tables into the SQLite version
galaxy prune-gxit-routes Prunes dead routes

galaxy amqp-test

(source) galaxy amqp-test - Test a given AMQP URL for connectivity

SYNOPSIS

gxadmin galaxy amqp-test <amqp_url>

NOTES

Note: must be run in Galaxy Virtualenv

Simple script to test an AMQP URL. If connection works, it will immediately exit with a python object:

$ gxadmin galaxy amqp-test pyamqp://user:pass@host:port/vhost
<kombu.transport.pyamqp.Channel object at 0x7fe56a836290>

$ gxadmin galaxy amqp-test pyamqp://user:pass@host:port/vhost?ssl=1
<kombu.transport.pyamqp.Channel object at 0x7fe56a836290>

Some errors look weird:

wrong password:

$ gxadmin galaxy amqp-test ...
Traceback
...
amqp.exceptions.AccessRefused: (0, 0): (403) ACCESS_REFUSED - Login was refused using authentication mechanism AMQPLAIN. For details see the broker logfile.

wrong host, inaccessible host, basically any other problem:

$ gxadmin galaxy amqp-test ...
[hangs forever]

Basically any error results in a hang forever. It is recommended you run it with a timeout:

$ timeout 1 gxadmin galaxy amqp-test
$

galaxy cleanup

(source) galaxy cleanup - Cleanup histories/hdas/etc for past N days (default=30)

SYNOPSIS

gxadmin galaxy cleanup [days]

NOTES

Cleanup histories/hdas/etc for past N days using the python objects-based method

galaxy cleanup-jwd

(source) galaxy cleanup-jwd - (NEW) Cleanup job working directories

SYNOPSIS

gxadmin galaxy cleanup-jwd <working_dir> [1|months ago]

NOTES

Scans through a provided job working directory subfolder, e.g. job_working_directory/ without the 005 subdir to find all folders which were changed less recently than N months.

Then it takes the first 1000 entries and cleans them up. This was more of a hack to handle the fact that the list produced by find is really long, and the for loop hangs until it's done generating the list.

galaxy decode

(source) galaxy decode - Decode an encoded ID

SYNOPSIS

gxadmin galaxy decode <encoded-id>

NOTES

Encode an unecoded ID

$ GALAXY_CONFIG_FILE=/srv/galaxy/config/galaxy.yml GALAXY_ROOT=/srv/galaxy/server gxadmin galaxy decode 6fe4eea8c591a9c4
123

galaxy encode

(source) galaxy encode - Encode an ID

SYNOPSIS

gxadmin galaxy encode <encoded-id>

NOTES

Encode an unecoded ID

$ GALAXY_CONFIG_FILE=/srv/galaxy/config/galaxy.yml GALAXY_ROOT=/srv/galaxy/server gxadmin galaxy encode 123
6fe4eea8c591a9c4

galaxy fav-tools

(source) galaxy fav-tools - Favourite tools in Galaxy DB

SYNOPSIS

gxadmin galaxy fav-tools

NOTES

What are people's fav tools

galaxy fix-conda-env

(source) galaxy fix-conda-env - Fix broken conda environments

SYNOPSIS

gxadmin galaxy fix-conda-env <conda_dir/envs/>

NOTES

Fixes any broken conda environments which are missing the activate scripts in their correct locations.

MUST end in /envs/

galaxy ie-list

(source) galaxy ie-list - List GIEs

SYNOPSIS

gxadmin galaxy ie-list

NOTES

List running IEs (based on output of queue-detail)

$ gxadmin local ie-list
running  6134209  jupyter_notebook  helena-rasche

galaxy ie-show

(source) galaxy ie-show - Report on a GIE [HTCondor Only!]

SYNOPSIS

gxadmin galaxy ie-show [gie-galaxy-job-id]

NOTES

The new versions of IEs are IMPOSSIBLE to track down, so here's a handy function for you to make you hate life a lil bit less.

$ gxadmin local ie-show 6134209
Galaxy ID: 6134209
Condor ID: 1489026
Container: jupyter_notebook
Running on: cn032.bi.uni-freiburg.de
Job script: /data/dnb01/galaxy_db/pbs/galaxy_6134209.sh
Working dir: /data/dnb02/galaxy_db/job_working_directory/006/134/6134209
Runtime:
{
  8888: {
    host: 132.230.68.65,
    port: 1035,
    protocol: tcp,
    tool_port: 8888
  }
}

Mapping
Key: aaaabbbbccccdddd
KeyType: interactivetoolentrypoint
Token: 00001111222233334444555566667777
URL: https://aaaabbbbccccdddd-00001111222233334444555566667777.interactivetoolentrypoint.interactivetool.usegalaxy.eu

It's probably only going to work for us? Sorry :)

galaxy migrate-tool-install-from-sqlite

(source) galaxy migrate-tool-install-from-sqlite - Converts SQLite version into normal potsgres toolshed repository tables

SYNOPSIS

gxadmin galaxy migrate-tool-install-from-sqlite [sqlite-db]

NOTES

$ gxadmin migrate-tool-install-from-sqlite db.sqlite
Migrating tables
  export: tool_shed_repository
  import: tool_shed_repository
  ...
  export: repository_repository_dependency_association
  import: repository_repository_dependency_association
Complete

galaxy migrate-tool-install-to-sqlite

(source) galaxy migrate-tool-install-to-sqlite - Converts normal potsgres toolshed repository tables into the SQLite version

SYNOPSIS

gxadmin galaxy migrate-tool-install-to-sqlite

NOTES

$ gxadmin migrate-tool-install-to-sqlite
Creating new sqlite database: galaxy_install.sqlite
Migrating tables
  export: tool_shed_repository
  import: tool_shed_repository
  ...
  export: repository_repository_dependency_association
  import: repository_repository_dependency_association
Complete

galaxy prune-gxit-routes

(source) galaxy prune-gxit-routes - Prunes dead routes

SYNOPSIS

gxadmin galaxy prune-gxit-routes <interactivetools_map>