Martin Čech -- 26.3.25 -- FI:PV269 Pokročilé metody bioinformatiky -- ELIXIR CZ / CESNET
If you take one thing from here be it that it's all at https://training.galaxyproject.org/
On March 29th, 2024, a backdoor was discovered in xz-utils, a suite of software that gives developers lossless compression. This package is commonly used for compressing release tarballs, software packages, kernel images, and initramfs images. It is very widely distributed, statistically your average Linux or macOS system will have it installed for
| // 3D Dom viewer, copy-paste this into your console to visualise the DOM as a stack of solid blocks. | |
| // You can also minify and save it as a bookmarklet (https://www.freecodecamp.org/news/what-are-bookmarklets/) | |
| (() => { | |
| const SHOW_SIDES = false; // color sides of DOM nodes? | |
| const COLOR_SURFACE = true; // color tops of DOM nodes? | |
| const COLOR_RANDOM = false; // randomise color? | |
| const COLOR_HUE = 190; // hue in HSL (https://hslpicker.com) | |
| const MAX_ROTATION = 180; // set to 360 to rotate all the way round | |
| const THICKNESS = 20; // thickness of layers | |
| const DISTANCE = 10000; // ¯\\_(ツ)_/¯ |
| # I ran each block individually by hand by pasting =P | |
| df -hl /var/lib/docker /var/jenkins && \ | |
| systemctl stop docker && \ | |
| umount /var/lib/docker && \ | |
| pkill -u jenkins | |
| # wait a few seconds, but not too long because Jenkins will reconnect D= | |
| umount /var/jenkins && \ |
Make sure nobody is running a docker container before restarting the service...
$ ssh [email protected]
$ cvmfs_server transaction main.galaxyproject.org
$ systemctl restart docker.service
$ docker run --rm -v /cvmfs:/cvmfs -p 127.0.0.1:8818:8888 galaxy/main_installer
| Backbone.js | |
| BlameHighlighter | |
| DocBlockr | |
| EasyDiff | |
| FileDiffs | |
| Git | |
| GitGutter | |
| Indent XML | |
| JSON Reindent | |
| LESS |
| --- from_file | |
| +++ untitled 1 | |
| @@ -9,13 +9,22 @@ | |
| from optparse import OptionParser | |
| parser = OptionParser() | |
| -parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) | |
| +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=None ) | |
| parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to fetch, or "all" for all eggs, even those not needed by your configuration' ) | |
| parser.add_option( '-p', '--platform', dest='platform', help='Fetch for a specific platform (by default, eggs are fetched for *this* platform' ) |
| 128.118.201.178 - - [05/May/2014:15:12:06 -0400] "PUT /api/histories/e89067bb68bee7a0/set_as_current HTTP/1.1" 200 - "http://martenson.bx.psu.edu:8080/library/list" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36" | |
| galaxy.web.framework ERROR 2014-05-05 15:13:07,230 Uncaught exception in exposed API method: | |
| Traceback (most recent call last): | |
| File "/Users/marten/marten-galaxy/lib/galaxy/web/framework/__init__.py", line 331, in decorator | |
| rval = func( self, trans, *args, **kwargs) | |
| File "/Users/marten/marten-galaxy/lib/galaxy/webapps/galaxy/api/histories.py", line 139, in set_as_current | |
| trans.history = history | |
| File "/Users/marten/marten-galaxy/lib/galaxy/web/framework/__init__.py", line 1022, in set_history | |
| self.galaxy_session.current_history = history |