- galaxy-dev - lists.galaxyproject.org

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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contribute to tools without github
by Matthias Bernt 20 Oct '17

20 Oct '17

I noticed that the sparql_uniprot tool does not run (python3 incompatibility). Since there is no github page I do not know how to contribute to such a tool. I have a similar problem with the lefse tool. What would be the best way to fix sich tools? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Re: [galaxy-dev] galaxy-dev Digest, Vol 136, Issue 11
by Matthias Enders 20 Oct '17

20 Oct '17

Dear Galaxy-Dev List, the problem disappeared this day, as our IT was rebuilding the whole with galaxy-docker container. Mit freundlichen Grüßen Matthias Enders ----------------------------------------------------------------------- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.enders(a)german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request(a)lists.galaxyproject.org Gesendet: Mittwoch, 18. Oktober 2017 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 136, Issue 11 Priorität: Hoch Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner(a)lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Problems with the test tool shed? (Von Kuster, Greg) 2. Re: Problems with the test tool shed? (Martin Čech) 3. Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8 (Hans-Rudolf Hotz) 4. Re: MACS2 Error (Deepak Tanwar) 5. Re: MACS2 Error (Devon Ryan) 6. Problems with BlastDB.loc (Enders Matthias) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Oct 2017 18:21:40 +0000 From: "Von Kuster, Greg" <ghv2(a)psu.edu> To: "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: [galaxy-dev] Problems with the test tool shed? Message-ID: <9CCD9F8D-D91A-43AA-9F88-D7D777777AC9(a)mymail.psu.edu> Content-Type: text/plain; charset="utf-8" Hi all, I’m wondering if the TTS can be restarted. I’ve been seeing this of-and-on all afternoon. Thanks! Galaxy<http://galaxyproject.org/> The Test Tool Shed could not be reached You are seeing this message because a request to The Test Tool Shed timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please contact an administrator. -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171017/1…> ------------------------------ Message: 2 Date: Tue, 17 Oct 2017 18:56:28 +0000 From: Martin Čech <marten(a)bx.psu.edu> To: "Von Kuster, Greg" <ghv2(a)psu.edu>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Problems with the test tool shed? Message-ID: <CAHKBquHKS5zeCwc++8+BCvnqpRHtnowUTk0s62b9KTg6Et4iYQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Done, seems up now. Thanks for the report. M. On Tue, Oct 17, 2017 at 2:22 PM Von Kuster, Greg <ghv2(a)psu.edu> wrote: > Hi all, > > I’m wondering if the TTS can be restarted. I’ve been seeing this > of-and-on all afternoon. > > Thanks! > > Galaxy <http://galaxyproject.org/> > The Test Tool Shed could not be reached > > You are seeing this message because a request to The Test Tool Shed > timed out or was refused. This may be a temporary issue which could be > resolved by retrying the operation you were performing. If you receive > this message repeatedly or for an extended amount of time, please > contact an administrator. > > ___________________________________________________________ > 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171017/f…> ------------------------------ Message: 3 Date: Wed, 18 Oct 2017 08:56:17 +0200 From: Hans-Rudolf Hotz <hrh(a)fmi.ch> To: Matthias Enders <m.enders(a)german-seed-alliance.de>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8 Message-ID: <59E6FB11.4080900(a)fmi.ch> Content-Type: text/plain; charset="utf-8"; format=flowed On 10/17/2017 05:02 PM, Matthias Enders wrote: > Hi Hans, > > your right, I´ve checked this. The utils are free and the folder on > GITHub contains the tools needed. Perhaps it´s an idea to change the > link on the website (https://galaxyproject.org/visualization-setup/) > from here ("http://hgdownload.cse.ucsc.edu/admin/exe/") > to github? > ("https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils") like the whole galaxy project, the Galaxy hub pages are a community effort. So feel free to improve the page yourself by making a adding the github page as a second resource for the faToTwoBit tool. Hans-Rudolf > > Mit freundlichen Grüßen > > Matthias Enders > ---------------------------------------------------------------------- > - > > > GERMAN SEED ALLIANCE GmbH > c/o Norddeutsche Pflanzenzucht > Hans-Georg Lembke KG > Hohenlieth, 24363 Holtsee > Tel.: +49 (0)4351/ 736-189 > Fax: + 49 (0)4351/ 736-271 > Mobil: +49 (0)151/ 14247360 > > Email: m.enders(a)german-seed-alliance.de > > Firmensitz Köln > Amtsgericht Köln, HRB 73844 > > -----Ursprüngliche Nachricht----- > Von: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] > Gesendet: Dienstag, 17. Oktober 2017 16:50 > An: Matthias Enders <m.enders(a)german-seed-alliance.de>; > galaxy-dev(a)lists.galaxyproject.org > Betreff: Re: AW: the future of trackster - was: galaxy-dev Digest, Vol > 136, Issue 8 > > Hi Matthias > > No, the twobit-files are not mandatory for trackster. They are only required if you want to zoom into the nucleotide level. > > Also, though, I am not sure, and I recommend to check this with your legal department, but I have been under the impression that the tool 'faToTwoBit' can be built from the "kent/src/utils" source code directory, which is freely available for all uses, isn't-it? > > > Regards, Hans-Rudolf > > > > > On 10/17/2017 04:29 PM, Matthias Enders wrote: >> Hi Hans, >> >> actually we are a company and the UCSC Genome Browser is not freely >> available for us. As you pinpointed me to the website: >> https://galaxyproject.org/visualization-setup/ >> >> There is an link to USCS utilities (for creating twobitfiles) >> (http://hgdownload.cse.ucsc.edu/admin/exe/) >> Actually this tools are also under license agreements, that permits free commercial download or usage. >> >> If I understand it correctly the twobit-files are mandatory for trackster, implicating that we have to buy licenses for using UCSC Genome Browser and/or Trackster? >> >> If yes: Are there any attempts to build in or rebuild this utilities, so the full project with all parts "remains" compatible with AFL3 license? >> >> Mit freundlichen Grüßen >> >> Matthias Enders >> --------------------------------------------------------------------- >> - >> - >> >> >> GERMAN SEED ALLIANCE GmbH >> c/o Norddeutsche Pflanzenzucht >> Hans-Georg Lembke KG >> Hohenlieth, 24363 Holtsee >> Tel.: +49 (0)4351/ 736-189 >> Fax: + 49 (0)4351/ 736-271 >> Mobil: +49 (0)151/ 14247360 >> >> Email: m.enders(a)german-seed-alliance.de >> >> Firmensitz Köln >> Amtsgericht Köln, HRB 73844 >> >> -----Ursprüngliche Nachricht----- >> Von: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] >> Gesendet: Dienstag, 17. Oktober 2017 10:33 >> An: Matthias Enders <m.enders(a)german-seed-alliance.de>; >> galaxy-dev(a)lists.galaxyproject.org >> Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136, >> Issue 8 >> >> Hi Matthias >> >> We had a Birds of a Feather session about (the future of) Trackster at the recent galaxy community conference in Montpellier. Though, as far as I know (I might be wrong), this didn't result in any no active development on the Trackster code. >> >> What kind of functionality do you miss? It might be worth rising an issue on github (https://github.com/galaxyproject/galaxy/issues) ? >> >> >> Personally, I consider Trackster and the option to display data at >> the UCSC genome browser as two different pairs of shoes: >> >> - Trackster is a easy option to look at your data quickly. It is >> particular useful, if you work with non-model organisms >> >> - the display of your data at UCSC is handy, if you want to >> visually compare it with all the available UCSC tracks. However, keep >> in mind, unless you are using a local copy of the UCSC gemome >> browser, the data will leave your local network. >> >> >> >> WRT tutorial: Have you seen these pages: >> >> https://galaxyproject.org/learn/visualization/ >> https://galaxyproject.org/visualization-setup/ >> >> >> Regards, Hans-Rudolf >> >> >> PS: I took the freedom to change the subject line for easier >> searching in the future >> >> >> >> >> >> >> On 10/16/2017 03:50 PM, Matthias Enders wrote: >>> Dear Galaxy Dev List, >>> >>> we currently searching for a good Genome Browser. As we run a local galaxy instance, we noticed the integrated GTB ("Galaxy Track Browser"). >>> >>> So my question is: Is there a roadmap for further support / development of the GTB? >>> >>> Or will it perhaps get replaced/deprecated in the near future (we read a lot of UCSC Genome Browser - Galaxy - Integration)? >>> >>> Another question would be on good sources/tutorials/manuals for configuring and setup for the GTB. >>> >>> Mit freundlichen Grüßen >>> >>> Matthias Enders >>> -------------------------------------------------------------------- >>> - >>> -- >>> >>> >>> GERMAN SEED ALLIANCE GmbH >>> c/o Norddeutsche Pflanzenzucht >>> Hans-Georg Lembke KG >>> Hohenlieth, 24363 Holtsee >>> Tel.: +49 (0)4351/ 736-189 >>> Fax: + 49 (0)4351/ 736-271 >>> Mobil: +49 (0)151/ 14247360 >>> >>> Email: m.enders(a)german-seed-alliance.de >>> >>> Firmensitz Köln >>> Amtsgericht Köln, HRB 73844 >>> ___________________________________________________________ >>> 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/ >>> ------------------------------ Message: 4 Date: Wed, 18 Oct 2017 15:46:25 +0000 From: Deepak Tanwar <dktanwar(a)hotmail.com> To: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] MACS2 Error Message-ID: <DM5PR0201MB3622F9AECC91FB13134EBB11DF4D0(a)DM5PR0201MB3622.namprd02.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar(a)hotmail.com<mailto:dktanwar@hotmail.com>> wrote: Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] gawk 4.1.3 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] Thank you, Deepak -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/1…> ------------------------------ Message: 5 Date: Wed, 18 Oct 2017 17:51:48 +0200 From: Devon Ryan <dpryan79(a)gmail.com> To: Deepak Tanwar <dktanwar(a)hotmail.com>, Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] MACS2 Error Message-ID: <5592e574-694c-fe3a-ce13-5e340e73627e(a)gmail.com> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Assuming you don't have galaxy set to clean up job working directories upon failure, have a look at the tool_script.sh in that directory and see if you can discern the issue. Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful. Devon On 10/18/2017 05:46 PM, Deepak Tanwar wrote: > Hello, > > I am still facing problem. I have tried to reinstall MACS2 but nothing > helped. > > Thank you! > Deepak > > >> On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar(a)hotmail.com >> <mailto:dktanwar@hotmail.com>> wrote: >> >> Hi all, >> >> There is some problem with MACS2: >> >> export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: >> line 25: macs2: command not found Fatal error: Exit code 127 () Tool >> installed: >> /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 >> <http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> >> >> Dependency Resolver Details >> Dependency Version Resolver Exact version Current Installation >> Status >> macs2 2.1.1.20160309 Conda True >> gawk 4.1.3 Conda True >> >> >> >> Thank you, >> Deepak > > > > ___________________________________________________________ > 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/ -- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79(a)gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/c…> ------------------------------ Message: 6 Date: Wed, 18 Oct 2017 07:02:44 +0000 From: Enders Matthias <m.enders(a)npz-innovation.de> To: "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: [galaxy-dev] Problems with BlastDB.loc Message-ID: <61B3F546DFD52B46B25883C23E2FF9DA294048BC(a)MAIL.npz.local> Content-Type: text/plain; charset="iso-8859-1" Dear Galaxy Dev List, we currently facing a problem with integrating new Blast Databases in our Galaxy instance. We added a the new DB to the file: /galaxy-central/tool-data/blastdb.loc But the new Database didn't show up in the respective tools, this situation remains also after restarting the galaxy instance and reloading the tool config (blasn for example). As we included several databases before (which worked fine) we tried to find the error an excluded (out-commented) an existing Db, but this database stayed in the tools. So the blastdb.loc file seems to be ignored by galaxy. (This is consistent for multiple users and browser, so we are sure this is not a client-sided Browser-Cache issue) So my questions are: Is there any kind of internal Cache in Galaxy which could explain this behavior? How can we track down / solve the issue? Our Galaxy Version is 17.05 Thanks a lot in advance! Mit freundlichen Grüßen i.A. Matthias Enders ********************************** [cid:image002.png@01CF9B54.EBA59810] NPZ Innovation GmbH Hohenlieth-Hof, D-24363 Holtsee Tel. +49-4351-736 189<tel:%2B49-4351-736%20189> Fax +49-4351-736 271<tel:%2B49-4351-736%20271> Mobil: +49-151-14247360<tel:%2B49-0151-14247360> Mail: m.enders(a)npz-innovation.de<mailto:m.enders@npz-innovation.de> Web: www.npz-innovation.de<http://www.npz-innovation.de/> Firmensitz Hohenlieth, Holtsee Amtsgericht Kiel, HRB 15342 Kl Geschäftsführer: Dr. Gunhild Leckband, Thorsten Pommer -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/5…> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 6168 bytes Desc: image001.png URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/5…> ------------------------------ Subject: Digest Footer _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ------------------------------ End of galaxy-dev Digest, Vol 136, Issue 11 *******************************************

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error despite success
by Matthias Bernt 18 Oct '17

18 Oct '17

Dear list, today I got an erroneous result (red) despite the output of the tool to be seems fine. Seemingly there was an error during setting the metadata. ``` Fatal error: An error occured during execution, see stderr and stdout for more information Reading reference gene model /gpfs1/data/galaxy_server/galaxy-dev/database/files/002/dataset_2992.dat ... Done Loading SAM/BAM file ... Finished Total 62188 usable reads were sampled Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py", line 85, in set_metadata datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py", line 109, in load_datatypes tree = galaxy.util.parse_xml(config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", line 214, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW' ``` Are there any suggestions how to continue with such a behavior. The file system on our cluster seems to be slow at the moment, could this be the cause? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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