Re: [galaxy-dev] Failure in uploading datasets

On Thu, Dec 4, 2014 at 11:53 AM, David Matthews pa...@bristol.ac.uk wrote: HI, We have had a copy of Galaxy working on a login node on our cluster here for a few weeks. We have tried to get it to work with the queue but could not and so reverted back to the login node for now. However, when

Re: [galaxy-dev] Assertion errors when starting Galaxy

Hi Lance (and Ricardo), This is occurring because in the last release, some options from the Galaxy config file (ucsc_display_sites, gbrowse_display_sites) as well as the list of genome builds for other display applications (which was previously a path in the display application's XML file in

Re: [galaxy-dev] problems installing tool dependency

and then tell Galaxy the dependency is installed for the other Miller Lab tools? Thank you for any help you can provide. *From:* Nate Coraor [mailto:n...@bx.psu.edu] *Sent:* Wednesday, September 24, 2014 2:58 PM *To:* Will Holtz *Cc:* Sajdak, Doris; galaxy-...@lists.bx.psu.edu *Subject:* Re

Re: [galaxy-dev] Starting uWSGI

, just let me know. Thanks! On Wed, Jan 28, 2015 at 2:53 PM, Nate Coraor n...@bx.psu.edu wrote: On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline nx...@case.edu wrote: Hi Nate. Thank you for the reply. So I installed uWSGI inside my Python virtual environment since that was one of the options

Re: [galaxy-dev] Web/Job scaling question

Hi Josephine, The uWSGI setup is more robust, both in terms of scalability, and load balancing. I'd suggest it for any multiuser setup at this point. --nate On Mon, Jan 5, 2015 at 3:10 PM, Josephine Palencia josep...@psc.edu wrote: Hello, Current setup: : have 1-2 VMs w/ 4-core each,

Re: [galaxy-dev] galaxy and torque - resource allocation

Hi Edgar, I'd suggest checking your Apache logs to see if the upload was denied by the server configuration (possibly for being too large). Also, please try using the modal upload method to see whether the upload is actually completing. This can be found by clicking the icon of a box with an up

Re: [galaxy-dev] galaxy and torque - resource allocation

with the arrow going up constantly. Do you think it’s an apache configuration error or galaxy or both? Cordialement / Regards, Edgar Fernandez *De :* Nate Coraor [mailto:n...@bx.psu.edu] *Envoyé :* January-22-15 10:10 AM *À :* Fernandez Edgar *Cc :* John Chilton; galaxy

Re: [galaxy-dev] Starting uWSGI

your help. On Mon, Jan 26, 2015 at 5:22 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Nicholas, Sorry for the somewhat misleading text in the documentation. The part about no extra modules or recompiling refers to nginx itself - uWSGI protocol support is built in to the core functionality

[galaxy-dev] Galaxy Tool Shed security vulnerability

*Please note: This notice affects Galaxy Tool Shed servers only. Galaxy servers are unaffected.* A security vulnerability was recently discovered by Daniel Blankenberg of the Galaxy Team that would allow a malicious person to execute arbitrary code on a Galaxy Tool Shed server. The vulnerability

Re: [galaxy-dev] file_path passed directly to wrappers

On Wed, May 13, 2015 at 7:23 AM, Sabrina rodriguez sabrina.rodrig...@toulouse.inra.fr wrote: Dear all, I am integrating some tools into galaxy and I would like to use some of the paths from the file universe_wsgi.ini (ex:file_path) directly into my perl wrappers in order for my per script

Re: [galaxy-dev] Tool failure due to PYTHONPATH in job environment after upgrade to 15.03

Hi Brian, $PYTHONPATH was previously only modified when a tool's command line started with `python`. This somewhat arbitrary change was modified in ee1a2b8 to allow the external set_metadata process to run without requiring an absolute path to a script on disk. However, the job script template

Re: [galaxy-dev] missing auth_conf.xml.sample

Hi Tony, Sorry for the trouble, the file was missing due to changes in the config/* directory being excluded by .hgignore. The missing file (and one other) has been pushed to Bitbucket, so you should be able to `hg pull -u` to get a fixed version. --nate On Fri, May 15, 2015 at 2:35 PM, Dannon

[galaxy-dev] Galaxy Tool Shed Security Vulnerability - Repository uploads

*DESCRIPTION* A security vulnerability was recently discovered by Peter Cock at the James Hutton Institute that would allow a malicious actor to upload new versions to repositories on which they have not been granted access. *AFFECTED VERSIONS* This issue affects versions of the Tool Shed

[galaxy-dev] Galaxy Security Vulnerability - Authentication framework with LDAP

*DESCRIPTION* A security vulnerability was recently discovered by Nicola Soranzo at The Genome Analysis Centre that would allow unauthorized access to Galaxy accounts on Galaxy servers using the LDAP authentication framework plugin. This is due to the fact that LDAP may be configured to allow

Re: [galaxy-dev] ./run.sh segfault

Hi Martin, Is there anything in the syslog? --nate On Thu, Jul 16, 2015 at 11:26 AM, Martin Vickers mj...@aber.ac.uk wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi All, I have a weird issue that's just cropped up. After a new install of galaxy (checked out on Monday from

Re: [galaxy-dev] Slow repsonses viewing histories

-detect. --nate On Wed, Jul 15, 2015 at 3:16 PM, Poole, Richard r.po...@ucl.ac.uk wrote: Hi Nate, I am indeed using later than 15.05………so I will try this fix next time I can restart the server and let you know. Richard On 15 Jul 2015, at 19:32, Nate Coraor n...@bx.psu.edu wrote: Hi

Re: [galaxy-dev] Nob able to upload even 25MB of file for running metaphlan on public Galaxy sever.

On Thu, Jul 9, 2015 at 1:25 PM, Prathik KV prathikkv_1...@yahoo.co.in wrote: Hi, I am trying to run metaphlan on the Galaxy public website, but even a 25MB file cannot be uploaded for analysis. It says the size is too large. And to run metaphlan on local it is just a nightmare because there

Re: [galaxy-dev] Galaxy configuration

Hi Clinton, On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee wrote: > Dear Galaxy devs / support, > > I am trying to understand the following snippet from job_conf.xml (I want > to use drmaa v1) > > > galaxy@merc > > > > > Based on someone's

Re: [galaxy-dev] SFTP configuration with ProFTPD

On Tue, Sep 8, 2015 at 2:05 PM, Jose Juan Almagro Armenteros < jjalma...@gmail.com> wrote: > Hello everyone, > > I am a bit stuck trying to set up a SFTP on my local Galaxy. I already > have an FTP server as described in the Galaxy wiki and in this post " >

Re: [galaxy-dev] dramm.py error

On Thu, Feb 4, 2016 at 1:21 PM, Le-shin Wu wrote: > Hi, > > I was trying to setup a galaxy server and connect to our UGE cluster. If I > setup the default job runner as "local", our galaxy server works properly. > But if I change the default job runner as "drmaa", our galaxy

Re: [galaxy-dev] Gemini installation error

On Thu, Feb 11, 2016 at 12:43 PM, Sebastian Schaaf < sch...@ibe.med.uni-muenchen.de> wrote: > Hey all, > > I am currently trying to install Gemini (v0.18.1) via the test toolshed. > It finally fails in dependencies as 'package_gemini_0_18_1' finds > dependency 'gemini' to end in error state.

Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

On Mon, Feb 22, 2016 at 5:54 AM, Peter Cock wrote: > Hi all, > > Last week at the Galaxy Admins video hangout Nate gave an > overview of the way Python dependency handling is changing > from using egg files to using wheel files instead - slide links at: > >

[galaxy-dev] Galaxy Security Vulnerability - Read/write arbitrary filesystem paths, arbitrary code execution

*DESCRIPTION* Multiple security vulnerabilities were recently discovered in Galaxy that allow malicious actors to read and write files on the Galaxy server. Additionally, Galaxy servers on which a rarely used feature has been enabled are vulnerable to an arbitrary code execution exploit. 1. A

[galaxy-dev] Galaxy/Tool Shed Security Vulnerability - Read/write arbitrary filesystem paths

*DESCRIPTION* Multiple security vulnerabilities were recently discovered in the Tool Shed that allow malicious actors to read and write files on the Tool Shed server outside of normal Tool Shed repository directories. 1. A write vulnerability exists in the Tool Shed tarball and capsule upload

Re: [galaxy-dev] Galaxy 16.01, eggs vs wheels, and running jobs as the user

On Tue, Feb 23, 2016 at 4:04 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Mon, Feb 22, 2016 at 9:02 PM, Nate Coraor <n...@bx.psu.edu> wrote: > > On Mon, Feb 22, 2016 at 5:54 AM, Peter Cock <p.j.a.c...@googlemail.com> > > wrote: > >> > >&g

Re: [galaxy-dev] Seeking Job Metrics Clarity

On Wed, Feb 24, 2016 at 5:37 AM, Ziphozakhe Mashologu wrote: > Hi All > > I have enabled job metrics on a local galaxy install, with latest code > from dev branch. I have " " uncommented in job_metrics_conf.xml > file: > > Following are the errors in the logs: > >

Re: [galaxy-dev] Missing modules after upgrade to 16.01

Hi Cristian, It's up to you whether you keep it with Galaxy or not. I prefer not to modify the Galaxy clone at all so I keep it outside. More details about keeping the virtualenv separate can be found here in the documentation:

Re: [galaxy-dev] "\${GALAXY_SLOTS:-4}" usage help

is a variable for use in tool configuration files (and should probably default to "1", not "4"). When configuring a Galaxy server, you should not have to manipulate the $GALAXY_SLOTS variable directly. --nate > Thanks, > Richard > > > On 8 Apr 2016, at 15:05, N

Re: [galaxy-dev] "\${GALAXY_SLOTS:-4}" usage help

On Fri, Apr 8, 2016 at 9:55 AM, Poole, Richard wrote: > Could somebody point me to a good explanation of how to setup and use > GALAXY_SLOTS correctly on my server? > > A basic explanation is good but I also make use of Pulsar to stage some > jobs on our cluster here (my

Re: [galaxy-dev] Galaxy 15.10 Jobs not running

On Tue, Mar 1, 2016 at 1:19 PM, Ryan G wrote: > Hi all - We recently merged in Galaxy 15.10 changes into our staging > instance and have noticed jobs are no longer dispatched. There is no > obvious problem in the log file. > > I see in github, commits have recently

Re: [galaxy-dev] trouble with python packages after galaxy update

On Thu, Mar 3, 2016 at 3:24 AM, Linda Bakker wrote: > Hi Guys, > So i updated my galaxy instance to release_16.01 > I usually started galaxy in a venv and used pip to install any packages my > tool needed. (in this case, numpy and scipy) > > source

Re: [galaxy-dev] switch to git

On Thu, Mar 3, 2016 at 10:20 AM, Briand, Sheldon (NRC/CNRC) < sheldon.bri...@canada.ca> wrote: > Hi, > > > > I’ve done the recently announced security update for my running release > which is 15.01. I figured I had better switch to git now while I was at > it. However I’m having trouble

Re: [galaxy-dev] LDAP not working release 16_01

Hi Mohamed, You'll need to install the Python ldap module into Galaxy's virtualenv. This can be done with: /path/to/galaxy/.venv/bin/pip install python-ldap --nate On Tue, May 17, 2016 at 9:18 AM, Mohamed Kassam wrote: > Dear all, > I updated my galaxy this mornig to the

Re: [galaxy-dev] Using pbs-python with glibc version 2.12

er() > File "/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/ > python2.7/site-packages/pbs/pbs.py", line 22, in swig_import_helper > _mod = imp.load_module('_pbs', fp, pathname, description) > ImportError: /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/

Re: [galaxy-dev] Using pbs-python with glibc version 2.12

Hi David, It sounds like you may have installed the version of pbs-python currently in PyPI, which includes a copy of the Torque C library that is not "manylinux"-safe (it is not backwards compatible to older systems). The solution here is to install pbs-python from its source distribution: 1.

Re: [galaxy-dev] Compiling dependencies in galaxy yields error

t in > enumerated type \u2018gs_rop3_t {aka enum }\u2019 [-Wswitch] > case rop3_T: > ^ > In file included from ./base/gp_unix.c:19:0: > ./base/pipe_.h:41:1: warning: function declaration isn\u2019t a prototype > [-Wstrict-prototypes] > extern FILE *popen( /* const cha

Re: [galaxy-dev] Compiling dependencies in galaxy yields error

Hi Evan, Can you include the full error you're receiving? Thanks, --nate On Mon, Oct 31, 2016 at 10:11 AM, evan clark wrote: > I was installing a tool from the galaxy toolshed and one of the > dependencies was missing due to a bad link. I modified the install files to > use

[galaxy-dev] Galaxy Security Vulnerability - Arbitrary code execution

*DESCRIPTION* A security vulnerability was recently discovered by David Wyde in two Galaxy tools that are provided with and enabled by default in the Galaxy server. These vulnerabilities allow malicious actors to execute arbitrary code as the user running the Galaxy server. The vulnerable tools

[galaxy-dev] Announcing the October 2016 (v16.10) Galaxy Release

The Galaxy Committers team is pleased to announce the *October 2016 (v16.10) release of Galaxy *. Security

Re: [galaxy-dev] Errno 13 when trying to visualize Bowtie2 data

Hi Federico, This is due to a recent storage move on usegalaxy.org. We're working on this and it should be resolved soon. --nate On Wed, Nov 30, 2016 at 5:06 AM, Federico Miozzo wrote: > Hi, > > since few days, when trying to visualize my Bowtie2 data on IGV or UCSC,

Re: [galaxy-dev] Datasets incorrectly flagged as deleted

Lance, usegalaxy.org has 4,652,912 such datasets. The cause here is that deleting an entire history does not mark the HDAs deleted (so that if you view a deleted history you can see what datasets were deleted and which were not at the time of deletion). There is a separate hda.purged column that

Re: [galaxy-dev] Jobs don't run for one user

Hi Brad, Absolutely nothing about these jobs in the handler logs? --nate On Wed, Nov 30, 2016 at 8:20 PM, Langhorst, Brad <langho...@neb.com> wrote: > > On Nov 30, 2016, at 4:27 PM, Nate Coraor <n...@bx.psu.edu> wrote: > > Seems on the up 'n up. Can you check the `ha

Re: [galaxy-dev] Datasets incorrectly flagged as deleted

aps I'll need to write some script to check each of these to see if > the data does, indeed, exist, and then set the flag appropriately... Hrmm. > > Does anyone know what the `dataset.deleted` flag is used for? Is that just > supposed to be set when all `hda.purged` are `t`. Sort of l

Re: [galaxy-dev] Installation of packages failing

Hi Peter, Gildas, This was due to a power supply failure which we've fixed this morning, so this should all be working now. Thanks, --nate On Mon, Dec 19, 2016 at 5:46 AM, Peter Briggs wrote: > Hello Gildas > > I think the problem is more that the actual server

Re: [galaxy-dev] Speedup Galaxy

o debug = False > and activated the heartbeat. But I have no idea what the actual problem > was... > > I hope I can deactivate it soon, because it said that it will eat up > disk space rapidly... > > Cheers Jochen > > > On 12.12.2016 18:37, Nate Coraor wrote: > > Hi Joc

Re: [galaxy-dev] Tools pick up Python modules from Galaxy core rather than installed tool dependencies

Hi Peter, Thanks for posting your findings. You can also directly manipulate the PYTHONPATH in tags in job_conf.xml s, which may be enough, although this would be tedious for every dependency. --nate On Fri, Dec 16, 2016 at 5:35 AM, Peter Briggs wrote: > I

Re: [galaxy-dev] Fwd: Fwd: Usegalaxy.org Data Rsync Connection refused

Hi Christopher, It's currently down due to a hardware failure. I hope to have it back up within the week. Sorry for the inconvenience. Thanks, --nate On Wed, Dec 14, 2016 at 3:14 AM, Christopher Previti < christopher.prev...@dkfz-heidelberg.de> wrote: > Dear all, > > I was wondering if anybody

Re: [galaxy-dev] Connection to mariaDB generates tables, but does not migrate information

Hi Evan, Migration only refers to the schema. Galaxy does not copy data between databases for you. You'll need to dump the data from your old database (sqlite?) and load it into the new one. We don't have instructions for this but most general guides for this conversion available on the web

Re: [galaxy-dev] Issue with SLURM-DRMAA

Hi Gwen, I'm not the canonical source for slurm-drmaa, although development on the original version has slowed and there haven't been any releases since the death of the previous principal maintainer at the Poznań Supercomputing and Networking Center. Since I have become a sort of partial

Re: [galaxy-dev] Decrease Galaxy polling of slurm?

Hi Phil, Unfortunately, there's no configurable for this. You can, however, modify the loop's sleep here: https://github.com/galaxyproject/galaxy/blob/d7a0fdfaa748ca427dda1cef74b81e253f1921d5/lib/galaxy/jobs/runners/__init__.py#L552 Hope this helps, --nate On Wed, May 24, 2017 at 10:40 AM,

Re: [galaxy-dev] Galaxy slurm error

slurm job exceeded some allocated > resource (memory, cpu, time) and slurm killed the job. > > David Hoover > HPC @ NIH > > On Jun 15, 2017, at 11:28 AM, Nate Coraor <n...@bx.psu.edu> wrote: > > Hi Evan, > > Are there any other details logged for this job? > > --n

Re: [galaxy-dev] drmaa job status

Hi Matthias, I can't speak for GridEngine's specific behavior because I haven't used it in a long time, but it's not surprising that jobs "disappear" as soon as they've exited. Unfortunately, Galaxy uses periodic polling rather than waiting on completion. We'd need to create a

Re: [galaxy-dev] Galaxy slurm error

Hi Evan, Are there any other details logged for this job? --nate On Thu, Jun 15, 2017 at 9:20 AM, evan clark wrote: > Has anyone ever encountered an error such as this when running galaxy with > slurm and submitting files for upload and unzip. > > slurmstepd: get_exit_code

Re: [galaxy-dev] Urgent help needed

e, all datasets, tool_shed and all tools were on > another location, so I still have them. He deleted only galaxy directory. > Of course, I had some local tools an wrappers there, but at least I hope I > can still do something. > > > Thanks once again! > > Best, > > Ma

Re: [galaxy-dev] Urgent help needed

Hi Marija, Wow, sorry to hear this. If the datasets themselves were removed, it's unlikely there'd be a way to get them back. Some filesystems do have undelete tools to attempt to recover data that has not yet been overwritten. If you can stop all activity on that filesystem while investigating

[galaxy-dev] GX-2017-0003: Unauthorized filesystem access via data source tools

*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-dev] GX-2017-0001: Limited Galaxy Data Library unauthorized filesystem access

*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.

[galaxy-dev] GX-2017-0002: Arbitrary code execution for Galaxy servers with Galaxy Interactive Environments enabled

*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

Re: [galaxy-dev] Cluster Install Path Errors

I think this error most commonly occurs when a virtualenv is used with a different python than the one it was created with. Is the cluster also running Ubuntu 14.04? If not, you can create a separate virtualenv for running tools using the instructions at:

Re: [galaxy-dev] Cluster Install Path Errors

g a common version in > the shared directory between the two filesystems. The job is correctly > being scheduled and completes, metadata is just not written. I’m certainly > open to any additional ideas. > > > > Thanks, > > John > > > > *From: *Nate Cor

Re: [galaxy-dev] Running toolshed on localhost is broken in release_17.09?

Hi Peter, This might be due to the switch from Paste to uWSGI for reports and tool shed applications in 17.09. I do see that when using the 17.09 default configuration (uWSGI with config/tool_shed.yml.sample), the static content is not configured to be served, so I submitted a fix for that here:

Re: [galaxy-dev] bigwig problem

Hi Jochen, I ran in to this yesterday, we're working on fixing it right now. It's due to this: https://github.com/bioconda/bioconda-recipes/issues/5430 And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage, which still points to the old versions. I have an update here:

Re: [galaxy-dev] firezilla not working

Hi Atanu and Antara, This output indicates that your connection has succeeded and you were able to authenticate, but the switch to passive mode has failed. This most often occurs due to firewalls which inspect packets sent to the FTP control port (21) in order to read the PASV command to

Re: [galaxy-dev] bigwig problem

What I ended up doing was downgrading MySQL to 5.6 in the affected environments. On Tue, Feb 20, 2018 at 4:51 AM, Jochen Bick <jochen.b...@usys.ethz.ch> wrote: > Thanks, nate, > > can you tell me one I can update? And what i need to update? > > Cheers Jochen > > On 15

Re: [galaxy-dev] Reinstall Galaxy by keeping database, database files and tools

Hi Jochen, Yes, this is possible. You shouldn't need to reinstall tools. Everything that Galaxy modifies is in (by default) three places on the filesystem (in addition to the database): 1. GALAXY_ROOT/database/ - especially GALAXY_ROOT/files/ (datasets) and GALAXY_ROOT/dependencies/ (tool

[galaxy-dev] Re: galaxy not running after galaxy.yml changes

Hi Jochen, Could you check the value of the 'dependency_resolvers_config_file' option and verify that the file it points at (by default, config/dependency_resolvers_conf.xml) is properly formatted? --nate On Thu, May 9, 2019 at 1:25 PM Jochen Bick wrote: > Hi all, > > we are testing a newly

[galaxy-dev] Re: Errors running jobs in Galaxy 16.01 with slurm-drmaa 1.1.0

Hi Phil, I followed up over on the Github issue, let's track it there and we can reply here for the sake of history once we figure out what's going on. Thanks, --nate On Thu, Sep 12, 2019 at 12:32 AM Philip Blood wrote: > Update: Nate Coraor pointed me to the drmaa-run utility in slurm-dr

[galaxy-dev] Re: Galaxy install problems

this example: https://github.com/galaxyproject/galaxy/blob/e74239e010ece4a4b22d7a6fe0f0f3d96b67001b/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L25 --nate > best, > Luc > > > Luc Cornet, PhD > Bio-informatician > Mycology and Aerobiology > Sciensano >

[galaxy-dev] Re: Galaxy install problems

On Wed, Jun 30, 2021 at 10:30 AM Luc Cornet wrote: > Dear Marius, > > Many thank for your feedback. > > I join to this email: the playbook, the pulsarservers.yml file and the log > of pulsar playbook. > > CLI plugin is for us the best solution since we have nothing to maintain. > DRMAA is not