galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00

Files

T

Nicola Soranzo 7fee81607c Add linting with ruff

ruff (https://github.com/charliermarsh/ruff) is a new and extremely fast
Python linter, written in Rust.
Ruff can be used to replace Flake8 (plus a variety of plugins), isort,
pydocstyle, yesqa, eradicate, pyupgrade, and autoflake.
Here ruff is added to our current linters (flake8, flake8-bugbear and isort)
while we assess its reliability.
I've not enabled the isort rules because many of the options we use are not
implemented yet. I have instead enabled the pyupgrade rules (a tool which I
run manually every few months).

Also:
- Fix new linting errors reported by ruff.

2023-01-16 14:34:56 +00:00

collect_sge_job_timings.sh

Add Assaf Gordon's collect_job_timings.sh script.

2011-07-21 13:55:24 -04:00

edu.psu.galaxy.GalaxyServer.plist

MacOS X daemon launcher:

2010-12-13 13:54:22 +10:00

galaxy_config_merger.py

Add linting with ruff

2023-01-16 14:34:56 +00:00

galaxy_reports.fedora-init

missing ;; in case stop

2016-03-11 20:43:24 +01:00

galaxy.fedora-init

paster.pid/log to galaxy.pid/log reference update

2017-12-15 15:34:47 +00:00

gls.pl

Add the "Galaxy ls" script to contrib/. Thanks, Simon McGowan.

2011-09-06 11:51:01 -04:00

README

Fedora(/RHEL/SL/CentOS) init script, thanks Brad Chapman!

2011-12-05 14:55:00 -05:00

README

CONTENTS
--------

edu.psu.galaxy.GalaxyServer.plist:

    This is the LaunchDaemon definition for OS X (pre-Snow Leopard?). Assuming
    that Galaxy is installed in the home directory of the user 'galaxy', run:
        mkdir /Users/galaxy/galaxy_dist/log
        sudo cp /Users/galaxy/galaxy_dist/contrib/edu.psu.galaxy.GalaxyServer.plist /Library/LaunchDaemons/
        sudo chown root:wheel /Library/LaunchDaemons/edu.psu.galaxy.GalaxyServer.plist
    Launch Galaxy with:
        sudo launchctl load /Library/LaunchDaemons/edu.psu.galaxy.GalaxyServer.plist
    Galaxy will now be started everytime the computer starts.
    Written and submitted by James Casbon.

galaxy.debian-init:

    init script for Debian/Ubuntu Linux.  Copy to /etc/init.d/galaxy, modify
    paths, and configure for start at boot with `update-rc.d galaxy defaults`.
    Also written and submitted by James Casbon.

galaxy.fedora-init:

    init script for Fedora/RedHat/Scientific Linux/CentOS.  Copy to
    /etc/init.d/galaxy, modify paths, and configure for start at boot with
    `chkconfig galaxy on`.  Written and submitted by Brad Chapman.

galaxy.solaris-smf.xml:

    SMF Manifest for Solaris 10 and OpenSolaris.  Import with `svccfg import
    galaxy.solaris-smf.xml`.

gls.pl:

    "Galaxy ls", for sites where Galaxy logins match system logins, this script
    can be used to list the filesystem paths to a user's history datasets.
    Requires site modifications.  Written and submitted by Simon McGowan.