October 2017 - galaxy-dev - lists.galaxyproject.org

Monitoring Dashboard for Galaxy
by evan clark 03 Sep '18

03 Sep '18

I remember there previously being an additional tool that ran on a different port from galaxy that allowed for monitoring of performance and jobs running. Is this tool still packaged with galaxy and if so how can it be activated.

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Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras 14 Mar '18

14 Mar '18

Dear Mohamed, Karim, galaxy-dev list, A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it... Wishing you a good week end. Cheers, Yvan -------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud(a)gmail.com> Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy +1 On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote: Dear all, I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy . Thanks in Advance, Mohamed ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

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GMOD hackathon before PAG San Diego in January
by Scott Cain 21 Nov '17

21 Nov '17

Hi all, This January before PAG on the Wednesday and Thursday before PAG (January 10-11) in San Diego we are planning a GMOD hackathon. We expect that participants will be interested in solving problems/creating solutions related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in another GMOD project, by all means, let us know! We expect this hackathon to overlap with the Tripal hackathon that is on January 11 (I'm pretty sure; right Stephen?) If you are interested in attending this hackathon, please let me know so I can be sure we have an appropriately sized space. And if you're coming for the pre-PAG hackathon, consider staying for PAG, since there is always a lot of GMOD-related content at the meeting! Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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November News: Blog, pubs, PAG, servers, tools, ...
by Dave Clements 31 Oct '17

31 Oct '17

Hello all, The November 2017 Galaxy News <https://galaxyproject.org/galaxy-updates/2017-11/> is out! - The Galactic Blog takes off <https://galaxyproject.org/galaxy-updates/2017-11/#the-galactic-blog> - Publications <https://galaxyproject.org/galaxy-updates/2017-11/#publications>: - The Galaxy Pub library surpasses 5,000 publications - 110 new pubs added in October, including 5 highlighted pubs - Upcoming events <https://galaxyproject.org/galaxy-updates/2017-11/#events> (9 this month) - Galaxy (and GMOD) at PAG XXVI <https://galaxyproject.org/galaxy-updates/2017-11/#galaxy-and-gmod-at-plant-…> - *PAG Early registration ends today.* - Public Galaxy Server News - 33 pubs in October <https://galaxyproject.org/galaxy-updates/2017-11/#public-servers-in-october…> using, referencing or about public Galaxy servers - Citations section <https://galaxyproject.org/galaxy-updates/2017-11/#citation-sections-added-t…> added to public server list - New public server: BF2I-MAP <https://galaxyproject.org/galaxy-updates/2017-11/#bf2i-map> - And the Language Analysis Portal <https://galaxyproject.org/galaxy-updates/2017-11/#almost-a-public-server-la…> too - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2017-11/#toolshed-contributions> - New releases <https://galaxyproject.org/galaxy-updates/2017-11/#releases> of StarForge and sequence_utils. And Other news <https://galaxyproject.org/galaxy-updates/2017-11/#other-news> too. See the full newsletter <https://galaxyproject.org/galaxy-updates/2017-11/>. Dave C and the Galaxy Team -- https://galaxyproject.org/ https://usegalaxy.org/

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bam_to_bigwig invalid syntax error
by Marco Tangaro 26 Oct '17

26 Oct '17

Dear experts, I've an issue with the bam_to_bigwig (brad-chapman) tool from the ToolShed. I've installed it using Conda to solve dependencies. When I run it on a bam file I get this error: Fatal error: Exit code 1 () File "/home/galaxy/shed_tools/ toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to…", line 41 print "Have %i references" % len(sizes) ^ SyntaxError: invalid syntax I had a look in the job working directory. In the tool_script.sh the conda environment set is "$CONDA_DEFAULT_ENV" = "/export/job_work_dir/000/6/conda-env" (just in my case). Sourcing the conda environment, the python version is (/export/job_work_dir/000/6/conda-env) (.venv) [galaxy@vnode-0 6]$ python --version Python 3.6.2 Which is not compatible with the "print" code that we have in the bam_to_bigwig.py wrapper, at line 41. Any idea? Am I missing something? Best regards, Marco.

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Metadata setting python dependencies
by Ulf Schaefer 26 Oct '17

26 Oct '17

Hi all After running the recommended update I am now on branch 17.09. As part of the update I set up a new virtual env running an additional python 2.7.6. My previous virtual env was running 2.6.6 which is a system requirement for Centos 6. All dependencies were installed and Galaxy starts fine, but no tools run. The error is always a variation of this: Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] Traceback (most recent call last): File "galaxy-dist/database/jobs_directory/000/418/418014/set_metadata_4LcsZv.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 19, in <module> import json ImportError: No module named json I put some debug output at the top of set_metadata.py and it is indeed running the correct python version from the virtual env. Needless to say I can import json just fine using that python version. Any ideas? Any help is greatly appreciated. Thanks Ulf -- Ulf Schaefer, PhD Bioinformatics Scientist Bioinformatics Unit - Infectious Disease Informatics National Infection Service Public Health England 61 Colindale Ave, London NW9 5EQ ulf.schaefer(a)phe.gov.uk http://www.gov.uk/phe Protecting and improving the nation’s health ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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GX-2017-0003: Unauthorized filesystem access via data source tools
by Nate Coraor 23 Oct '17

23 Oct '17

*DESCRIPTION* A medium severity security vulnerability in tools utilizing the Galaxy data source protocol was recently discovered by Dan Blankenberg. This vulnerability allows anyone able to run an external data source tool to add to their history any file that is readable by the user running Galaxy jobs on the host where the job runs. This is due to the Python urllib library's ability to operate on `file://` URLs and a failure to check for such URLs in the tool. This vulnerability has been assigned the disclosure ID GX-2017-0003. *AFFECTED VERSIONS* This vulnerability affects all known versions of Galaxy. *IMPACT* Many such "external data source" tools are provided with the Galaxy distribution and are enabled by default (most tools under the "Get Data" section of the tool panel), meaning that its exploitability is fairly high, as only one such tool needs to be enabled to be vulnerable, including any custom data source tools (any tool that uses `tools/data_source/data_source.py`). What files will be readable depends entirely upon what the job's user has access to read on the host(s) where jobs run. *SOLUTION* Per our security policies[1], we have created fixes for all affected versions of Galaxy. These have been committed to the corresponding `release_YY.MM` (and `dev`) branches in the Galaxy GitHub repository. Releases prior to 16.07 will remain vulnerable and should be updated to a supported release as soon as possible. Eric Rasche recently undertook a hardening of the Galaxy code base against common security mishaps.[2] This included changing most uses of `urllib` to `requests`, which does not operate on `file://` URLs. Although no exploits were identified at that time, we felt this work was of great enough importance to production Galaxy servers that we backported it to releases from 16.07 forward. Because of this, and the GX-2017-0001 and GX-2017-0002 vulnerabilities, administrators are strongly encouraged to update immediately, even if they do not believe their servers are vulnerable. *INSTRUCTIONS* The fixes are available on the `release_16.07` through `release_17.09` and `dev` branches in the Galaxy GitHub repository[3]. You can simply `git pull` or use your normal update procedure to get the changes. For the changes to take effect, *YOU MUST RESTART ALL GALAXY SERVER PROCESSES*. --nate (on behalf of the Galaxy Committers) [1] https://github.com/galaxyproject/galaxy/blob/dev/SECURITY_POLICY.md [2] https://github.com/galaxyproject/galaxy/pull/4604 [3] https://github.com/galaxyproject/galaxy/

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GX-2017-0002: Arbitrary code execution for Galaxy servers with Galaxy Interactive Environments enabled
by Nate Coraor 23 Oct '17

23 Oct '17

*DESCRIPTION* A high severity security vulnerability was recently discovered in Galaxy Interactive Environments (GIEs) by the Galaxy Committers Team. Anyone with a Galaxy account can exploit this vulnerability to execute arbitrary code on the Galaxy server as the user running the Galaxy server process. This is possible due to incorrect quoting of user-provided data passed to a shell execution context for the GIE `docker run` command. This vulnerability has been assigned the disclosure ID GX-2017-0002. *AFFECTED VERSIONS* This vulnerability affects Galaxy version 17.05 and later that have been configured to enable Galaxy Interactive Environments. *IMPACT* The vulnerability only affects Galaxy servers on which Galaxy Interactive Environments are enabled (by setting the `interactive_environment_plugins_directory` option in galaxy.ini). Because the vulnerability can be exploited to execute arbitrary code, the impact for affected servers is severe. Administrators of Galaxy servers where GIEs *are* enabled should update immediately. Administrators of Galaxy servers where GIEs are *not* enabled *should* update their servers to ensure they are not vulnerable should they enable GIEs at a later date, however, it is not critical to do so immediately. *SOLUTION* Per our security policies[1], we have created fixes for all affected versions of Galaxy. These have been committed to the corresponding `release_YY.MM` (and `dev`) branches in the Galaxy GitHub repository. The fix switches from using shell execution to direct execution with exec(3) and therefore is not susceptible to shell escaping exploits *INSTRUCTIONS* The fixes are available on the `release_17.05`, `release_17.09`, and `dev` branches in the Galaxy GitHub repository[2]. You can simply `git pull` or use your normal update procedure to get the changes. For the changes to take effect, *YOU MUST RESTART ALL GALAXY SERVER PROCESSES*. --nate (on behalf of the Galaxy Committers) [1] https://github.com/galaxyproject/galaxy/blob/dev/SECURITY_POLICY.md [2] https://github.com/galaxyproject/galaxy/

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GX-2017-0001: Limited Galaxy Data Library unauthorized filesystem access
by Nate Coraor 23 Oct '17

23 Oct '17

*DESCRIPTION* A medium severity security vulnerability in Galaxy Data Libraries was recently discovered by Jelle Scholtalbers, and in the course of investigating this vulnerability, we discovered multiple related attack vectors. This vulnerability allows the following unauthorized actions: 1. Any user that has been granted the permission to add datasets to a library, library folder, or to modify an existing library dataset (an "authorized user"), is able to import any file on the system that is readable by the user running the Galaxy server. 2. Anyone can create libraries and library folders (but not add datasets to them) This is possible due to incorrect checking of admin privileges and for symbolic links in the user's `user_library_import_dir`. Neither case can be exploited directly through the Galaxy UI, but both can be exploited through the API. Case #1 is not exploitable by any user who is not an "authorized user" or if none of `library_import_dir`, `user_library_import_dir`, and `allow_path_paste` (formerly `allow_library_path_paste`) are set in galaxy.ini. This vulnerability has assigned the disclosure ID GX-2017-0001. *AFFECTED VERSIONS* This vulnerability affects all known versions of Galaxy. *IMPACT* The more severe vulnerability (reading arbitrary files) can only be exploited by users with elevated library privileges, so its exploitability is limited to users whom the Galaxy server admin(s) presumably know and trust. The creation of arbitrary libraries and folders is a nuisance, but not in and of itself a security issue. *SOLUTION* Per our security policies[1], we have implemented fixes for versions of Galaxy from 16.07 through the forthcoming 17.09. These have been committed to the corresponding `release_YY.MM` (and `dev`) branches in the Galaxy GitHub repository. Releases prior to 16.07 will remain vulnerable and should be updated to a supported release as soon as possible. If your user `user_library_import_dir` or any of its parents are symlinks, user library imports will fail. You should put the fully canonicalized absolute path in this galaxy.ini option. Because the fix disallows symlinks in `user_library_import_dir` which point outside the user's particular subdirectory, and because some Galaxy admins may have found this to be a useful ability, we have created a new `user_library_import_symlink_whitelist` option in galaxy.ini that allows admins to configure directories to which symlinks should be allowed. However, please be aware that *any* user with library add/modify privileges and the ability to create symbolic links will be able to import from any whitelisted directory. There is no per-user restriction for whitelisted directories. *INSTRUCTIONS* The fixes are available on the `release_16.07` through `release_17.09` and `dev` branches in the Galaxy GitHub repository[2]. You can simply `git pull` or use your normal update procedure to get the changes. For the changes to take effect, *YOU MUST RESTART ALL GALAXY SERVER PROCESSES*. --nate (on behalf of the Galaxy Committers) [1] https://github.com/galaxyproject/galaxy/blob/dev/SECURITY_POLICY.md [2] https://github.com/galaxyproject/galaxy/

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Urgent help needed
by Durdevic, Marija 20 Oct '17

20 Oct '17

Dear developers, The colleague of mine mistakenly deleted my Galaxy installation (rm -rf *). Unfortunately there is no backup of complete installation. I have backup only configuration files. Is there any chance to fetch new Galaxy instance from git and to connect it to the old database? Or maybe any other suggestion what to do in such case? Many thanks in advance! Best, Marija Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024<tel:%2B43%20316%2F385-73024> Fax:+43 316/385-73009<tel:%2B43%20316%2F385-73009> Email: marija.durdevic(a)medunigraz.at<mailto:marija.durdevic@medunigraz.at> Email: marija.djurdjevic(a)klinikum-graz.at<mailto:marija.djurdjevic@klinikum-graz.at> Web: https://zmf.medunigraz.at/

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