Re: [galaxy-dev] 回复： Help testing Galaxy - new release is coming soon

Hello, you might want to look at https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/Dockerfile and other Bjoern's docker recipes: https://github.com/bgruening/docker-recipes M. On Mon, Dec 1, 2014 at 8:45 PM, Weiyan Shen shenw...@gmail.com wrote: Hi bjoern.gruening‍, It is

Re: [galaxy-dev] Question Regarding fetch_eggs c. vs pip

Hi guys, the latest sync of your fork with Galaxy stable was on 2013-02-08, according to: https://bitbucket.org/galaxycloud/galaxy/commits/all?page=10 This is the diff of fetch_eggs.py in between your version and galaxy-central: https://gist.github.com/martenson/f5bc887b1721732991e0 It doesn't

Re: [galaxy-dev] tool shed updates broken on my local server

Hi Anne, moving the whole Galaxy installation is a tough job and we do not really have a good process for it. Your problem is most probably caused by the inconsistency in the DB. The path to the shed_tool_conf.xml is stored there and the changes you made to the location of the installation did

Re: [galaxy-dev] tool shed updates broken on my local server

if such a script already exists? Or should I write it myself? Any guidance on where to start would be great. Many thanks in advance for your help. Cheers, Anne. On 30 Jan 2015, at 15:46, Martin Čech mar...@bx.psu.edu wrote: Hi Anne, moving the whole Galaxy installation is a tough job

Re: [galaxy-dev] Adding options to a tool

Hello Scott, the tool named 'tophat' has been migrated out of distribution to the Tool Shed over a year ago. Which means that if it is in your Galaxy and your Galaxy is newer than a year it must have been installed from the Tool Shed. Tool Shed acts like an app store for Galaxy Tools. The tophat

Re: [galaxy-dev] wrong validation message in toolshed

Hi Pieter, there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this line: code file=match_library.py /) After you

Re: [galaxy-dev] problem with revision updates for repositories.

Hello Anna, I was not able to replicate this issue. Can you please elaborate a little bit more on the setup your Galaxy has? Do you use proxy? After clicking the URL you sent I will get redirected properly, can you please try visiting the url to check whether you get redirected? If I understand

Re: [galaxy-dev] problem with revision updates for repositories.

Hi Anna, On Fri, Mar 27, 2015 at 10:39 AM Anna Terry iseegl...@googlemail.com wrote: I'm still having major issues with repo updates. 1) I'm getting this message for installing dependencies for package_samtools_1_1 that it says are missing: Error installing tool dependency ncurses version

Re: [galaxy-dev] Interested in GSOC idea Docker Swarm and Compose ask for advices.

Our full trello board can feel somewhat overwhelming so have a look at this card with the easiest ways to contribute: https://trello.com/c/eFdPIdIB/1773-easiest-ways-to-contribute Martin On Mon, Mar 2, 2015 at 11:23 AM Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Afe, it's usually a

Re: [galaxy-dev] FW: Adding a new web-service or perhaps a webapp to Galaxy

Hello Pieter, adding a controller to Galaxy's codebase is not possible through the Tool Shed. It would be very unsecure to allow such. However, reading your code ( https://gist.github.com/martenson/7ce1ddb19c199b2df61c) you should be able to convert this controller into an actual tool (data

Re: [galaxy-dev] Data Libraries

Hello Ryan, it is currently not possible to give users rights to create data libraries. However you can create the libraries for them and give them rights to create and manage subfolders (doing the same things but one level below). Would that address your goal? Martin On Thu, Apr 23, 2015 at

Re: [galaxy-dev] anybody seen this class of error before?

Hi Brad, this is known somewhat rare startup error. Please restart your Galaxy and it should go away. Dannon is tracking it down and this recent change might solve it: https://github.com/galaxyproject/galaxy/pull/128 Martin On Sun, Apr 19, 2015 at 2:53 PM Langhorst, Brad langho...@neb.com

Re: [galaxy-dev] Shared Data Library issues with permissions

Hi Carrie, in what step did you actually add the datasets to the folder? Also how did you add it? Thanks Martin On Thu, Apr 23, 2015 at 6:27 PM Ganote, Carrie L cgan...@iu.edu wrote: Hi Devs, Maybe I'm missing something, but I'm having trouble getting permissions right on the Data

Re: [galaxy-dev] Job submission failed

Hello Vipin, the request goes to index() method at galaxy/lib/galaxy/webapps/galaxy/api/tools.py I also see in console the 403 Forbidden https://galaxy.cbio.mskcc.org/api/tools/ when trying to upload. This is probably connected with the upload problems some users were having with your Oqtans

Re: [galaxy-dev] Difference between GitHub and Mercurial Galaxy download...

Galaxy migrated from mercurial(on Bitbucket) to git(on GitHub). If you are starting new production Galaxy going with GitHub (master branch) is a good choice. On Thu, Apr 16, 2015 at 4:03 PM Asma Riyaz asmariya...@gmail.com wrote: Hi, Is there a difference between the github and mercurial

Re: [galaxy-dev] Strange repository dependency behavior with toolshed-installed naive_variant_caller

: Hi Martin, Thanks for the prompt reply! My responses are inline below. On Tue, Feb 24, 2015 at 8:26 AM, Martin Čech mar...@bx.psu.edu wrote: Are you using Admin UI for installation or API scripts? The admin UI exclusively. Does the 'installed tool shed repos' page show multiple

Re: [galaxy-dev] Galaxy ToolShed Update Problem

+ and file path issues. When I started to deploy Galaxy last year, the requirement in the web page was Python 2.5 or something lower than 2.6 I used. I think that message need to be updated as well. Thanks in advance, Yours, Zhaozhen argparse At 2015-04-07 22:43:50, Martin Čech mar

Re: [galaxy-dev] FW: tophat2 failing to execute

of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW) From: Eleanor Morgan e.mor...@curtin.edu.au Date: Wednesday, 20 May 2015 1:44 pm To: Martin Čech mar...@bx.psu.edu Subject: Re: [galaxy-dev] tophat2 failing to execute Hello Martin, Thank you very much

Re: [galaxy-dev] Problem with set_user_disk_usage.py script

The script by default expects Galaxy config to be at config/galaxy.ini if you have Galaxy config in a diffferent place you can use the --config flag to specify path to it. The config location has been recently changed (from galaxy root folder and a different filename) - that is why the defaults

Re: [galaxy-dev] Functional Test Failures with 15.05

Hello Ryan, the recommended way to leverage tests included with Galaxy is to run individually the subsets you are interested in. The syntax can be found here: https://wiki.galaxyproject.org/Admin/RunningTests I can confirm that fresh checkout of -dev with 'sh run_tests.sh' (which runs only

Re: [galaxy-dev] cheetah chaet sheet

I usually check this page: http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTION00060 M. On Fri, Jun 19, 2015 at 4:34 PM Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi, someone knows a cheat sheet with all the commands supported by cheetah?

Re: [galaxy-dev] Galaxy API to upload files to data library

Hello Ryan, for interacting with libraries through the Bioblend: http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries for loading data to libraries form the Galaxy's system (e.g. after FTP upload, or when admin):

Re: [galaxy-dev] Galaxy API to upload files to data library

History Dataset Association. i.e. if you already have the dataset in history you can very easily import it to a data library. M. On Fri, Jun 26, 2015 at 1:23 PM Ryan G ngsbioinformat...@gmail.com wrote: What is HDA? Sent from my iPhone On Jun 26, 2015, at 1:10 PM, Martin Čech mar

Re: [galaxy-dev] Galaxy API to upload files to data library

need to figure out how to link to the datasets. Sent from my iPhone On Jun 26, 2015, at 1:24 PM, Martin Čech mar...@bx.psu.edu wrote: History Dataset Association. i.e. if you already have the dataset in history you can very easily import it to a data library. M. On Fri, Jun 26, 2015 at 1:23

Re: [galaxy-dev] Change in toolshed disallowing install of previous versions of tools?

Hi Aaron, this is most probably connected with a bug that we discovered today in the 'reset metadata for all my repositories' feature. Unfortunately we discovered it by running it on Main Tool Shed. We have an alternate (time consuming) way of fixing individual repos (like I just did for the

Re: [galaxy-dev] Change in toolshed disallowing install of previous versions of tools?

Martin, Aaron On Wed, Aug 12, 2015 at 5:10 PM, Martin Čech mar...@bx.psu.edu wrote: Hi Aaron, this is most probably connected with a bug that we discovered today in the 'reset metadata for all my repositories' feature. Unfortunately we discovered it by running it on Main Tool Shed. We have

[galaxy-dev] Call for Tool Shed Admins

Hi everybody, similar to the existing mailing list of Galaxy instance admins we are putting together a mailing list of admins of Tool Shed instances (especially the public ones) so if you administer one (or more) please respond to me privately and I will put you on it. Thank you very much.

Re: [galaxy-dev] Adding categories to Main

Dear Keith, I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment. Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when

Re: [galaxy-dev] feature request

Created it for you here: https://github.com/galaxyproject/galaxy/issues/1045 On Mon, Nov 9, 2015 at 4:39 PM Ryan G wrote: > Yes, I'll do it there. > > On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning > wrote: > >> Hi Ryan, >> >> can you

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, it seems you are hitting this fail: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#L124 which hints that the tool is not properly loaded in the toolbox. Did you restart the server and handlers after you installed the tool? I cannot help with the MySQL as we

Re: [galaxy-dev] FASTQ Groomer tool

Hi Edgar, Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart. I updated the wiki (

Re: [galaxy-dev] installable revisions for repository suite definitions

Hi Aaron, we touched this recently here: https://github.com/galaxyproject/tools-devteam/pull/267 I believe that if you specify the repository_dependencies.xml of your suite in the following way: http://toolshed.g2.bx.psu.edu; /> you will pin the exact revision of the tool

Re: [galaxy-dev] about galaxy

There are multiple fastq formats and some tools only accept a subset of it. Please have a look at the 'FASTQ Groomer' tool it should allow you to convert your datase to the fastq format you need. Thank you for using Galaxy Martin On Wed, Sep 2, 2015 at 12:52 PM Dong Liu wrote:

[galaxy-dev] July 2015 Galaxy Release (v 15.07)

The very-slightly-delayed July 2015 Galaxy Release is out! Full release notes: http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html Highlights * *Interactive Environments* - The interactive environments (IE) framework features several updates this release and Galaxy is now

Re: [galaxy-dev] Adding categories to Main

the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document: http://galaxy-iuc-standards.readthedocs.org/en/latest/ Thank you for using Galaxy. Martin On Fri, Aug 7, 2015 at 2:57 PM Martin Čech <

Re: [galaxy-dev] Documentation of Galaxy API metadata objects

Hi Clare, I am sorry but you seem to have found the best resources already. Namely 'what dictionary keys to expect...in a particular Galaxy version' is a hard problem with the current docs. :/ We could definitely do a better job providing example calls and responses in the docs with the code, so

Re: [galaxy-dev] Picard installation dependency issues

u> wrote: >> >>> Hi Martin, >>> >>> Thanks very much for your reply, and also to Marius. >>> >>> After some investigation, it appears that there is a firewall issue on >>> my Galaxy server which is preventing the download of the file via

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Hans: I have had trouble with el capitan and gcc lately, updating the xcode commandlinetools sometimes helps. $ xcode-select --install M. On Wed, Dec 2, 2015 at 7:30 PM Hans Rudolph wrote: > Hi, > > I use Mac OS X 10.11.1 (El Capitan) - I append terminal output during

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Awesome Marius, thank you very much for looking into this! M. On Fri, Dec 4, 2015 at 12:30 PM Marius van den Beek wrote: > Hello Hans (and other OS X users), > > I hope that the last remaining problem should be fixed now. > There is a new revision of package_r_3_2_1 and

Re: [galaxy-dev] Job is queued for imported dataset in library

Hello Makis, What is the newest version? Is it dev branch of github repo or release_15.10 ? Note: The admin interface for datalibs is deprecated, could you please also try using the new UI under Shared Data / Data Libraries. You will see options to import from directories (under 'add datasets'

Re: [galaxy-dev] security: brute force login

Amogelang: Needless to say that you probably want to protect on your webserver side (nginx is expected in the example by Dannon) as opposed to the Galaxy application side. If you are really serious about this you should probably ask in a different place than here e.g. at

Re: [galaxy-dev] how to access current user's apikey

Good morning, I hope there is not, because tool should not have access to user's credentials. If you explain a bit what are you trying to do we can probably be of more help. Thank you for using Galaxy. Martin On Sat, Dec 26, 2015 at 9:27 AM wrote: > Good morning

Re: [galaxy-dev] how to access current user's apikey or History Id

d morning Martin, > Then maybe it would be better, and easier?, to pass the History ID to a > mako file. Is there a galaxy predefined item for the History ID similar to > the Dataset_id that can be passed? > Thanks > bob > - Original Message - > From: Martin Čech <

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

Hello Léo, all tool are sincerely welcomed in the Galaxy Tool Shed. Good tutorial for tool writing is a part of Planemo documentation: https://planemo.readthedocs.org/en/latest/writing.html Planemo is a command line toolset aimed at helping tool developers like you getting their tools into

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Hans Rudolph, thanks to Marius van den Beek this issue should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299 These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository (

Re: [galaxy-dev] Picard installation dependency issues

Hello Scott, thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299 These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

Hi Ulf, you most probably want your tool to depend on package_python_2_7_10 from the iuc (it will ensure your tool has access to 2.7.10 no matter what python the Galaxy executing your tool is using) The package is being developed here

Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?

Hello Malcolm, encoded_id is a database row id that has been ran through this method ( https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__init__.py#L46) using the 'secret' from galaxy.ini config. You should be able to do something like this in the mako:

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

t; http://www.ensembl.org/galaxy-dev.fmi.ch/tool_runner/biomart?type=text=Homo%20sapiens%20genes%20%28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/7ee294b9ae51a27f1e7ed96e712c5792?do_export=1=1 > > > > Hans-Rudolf > > > On 06/08/2016 04:36 PM, Martin Čech wrote: > >

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

The correct link is this: http://galaxy-dev.fmi.ch/tool_ runner/biomart?type=text=Homo%20sapiens%20genes%20% 28GRCh38.p5%29=http://www.ensembl.org/biomart/martview/ 7ee294b9ae51a27f1e7ed96e712c5792? On Wed, Jun 8, 2016 at 11:33 AM Martin Čech <mar...@bx.psu.edu> wrote: > This l

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

Hello Hans-Rudolf, What version of Galaxy are you using? Can you please share a specific URL you were sent to that returns a 404? thanks M. On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz wrote: > Hi all > > Please allow me to come back to this old problem: > > On

Re: [galaxy-dev] bx-python issue with intersect and subtract tools

Hello Richard, this issue has been solved, if you update the tool it should work as expected. Details are available here: https://biostar.usegalaxy.org/p/15974/ Thank you for using Galaxy Martin On Tue, Dec 1, 2015 at 5:28 PM Poole, Richard wrote: > Hi all, > > I just

Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

Hi Amos, what Galaxy are you using and where are you seeing these messages? thanks Martin On Thu, Jan 28, 2016 at 2:56 PM Raphenya, Amogelang wrote: > Hi All, > > Is there a faster way to upload or load large datasets into galaxy history > without using FTP? > > I tried

Re: [galaxy-dev] Working on the admin interface: JS vs Mako

Hi, Galaxy is implementing frontend with the help of these libraries: https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/libs Notably the MV-paradigm is being implemented in Backbone. Good examples of applications/pieces that are written in JS are at

Re: [galaxy-dev] Get data via the cloud?

Hi Scott, Galaxy can retrieve data from any publicly available URL. Just paste the URL into the upload modal using the 'paste/fetch data'. This probably won't work with some of the services as they won't serve you content without visiting their site. But it works with e.g. dropbox if you add

Re: [galaxy-dev] errors installing tool dependencies...

> My Sincere Salutations, > > > > *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la Communication > > *Université de Montréal* > > > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. :

Re: [galaxy-dev] errors installing tool dependencies...

bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568* > > > > > > *From:* Fernandez Edgar > *Sent:* January-25-16 11:11 AM > *To:* 'Martin Čech' <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu > *Subject:* RE: [galaxy-dev] errors installing tool dependencies...

Re: [galaxy-dev] Want to Contribute in galaxy project

Hi Manish, thank you very much for your interest in Galaxy project! I would first look here to check the beginner's dev overview: https://wiki.galaxyproject.org/Develop/GettingStarted And once you feel somewhat comfortable you can check the beginner friendly issues on GitHub here:

Re: [galaxy-dev] errors installing tool dependencies...

cola Soranzo [mailto:nicola.sora...@gmail.com > <nicola.sora...@gmail.com>] *On Behalf Of *Nicola Soranzo > *Sent:* January-25-16 12:05 PM > *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca> > <edgar.fernan...@umontreal.ca>; Martin Čech <mar...@bx.psu.edu> > &l

Re: [galaxy-dev] configuration management, tool shed and tool revisions

Hello Steve, Galaxy project's efforts in automating tool installations are mostly represented by the following Ansible playbook ( https://github.com/afgane/galaxy-tools-playbook) and a role ( https://github.com/galaxyproject/ansible-galaxy-tools). We plan on improving that tracked at:

Re: [galaxy-dev] Sample tracking / external services - still supported?

Hello Matthias, As you correctly identified the original implementation, in spite of being present in the Galaxy distribution, is treated as deprecated. However I know about three sample tracking implementation based on Galaxy's old sample tracking. - *TRON Mainz*

Re: [galaxy-dev] copy/import shared history

this “copy shared > history” function. Thanks for your information. > > Best > > Le-Shin > > > On Feb 16, 2016, at 1:02 PM, Martin Čech <mar...@bx.psu.edu> wrote: > > Hi LW, > > 1) The described 'copy' feature works well for me on usegalaxy.org. > However t

Re: [galaxy-dev] Please help fix toolshed repository: trtr

Hi Lance, it seems the whole .git/ folder got accidentally uploaded there and it causes trouble. I recommend using the direct mercurial access ( https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the folder, commit the change and push it to the TS repository. Please let me know how it

Re: [galaxy-dev] Request help to configure local galaxy in Git

Hi Manonanthini, Windows is not a supported platform for Galaxy and we do not have any official tutorials, tests or even proofs that it can be done. I recommend you run a virtual machine with a Linux image and install Galaxy there. Depending on what you want to do you can grab our pre-populated

Re: [galaxy-dev] Using forms to collect user info at registration

Hello Peter, you are right, this seems broken, sorry about that. I have created an issue to track the resolution of this bug: https://github.com/galaxyproject/galaxy/issues/1937 Thank you for reporting it. Martin On Wed, Mar 16, 2016 at 10:16 AM Peter Briggs

Re: [galaxy-dev] Please help fix toolshed repository: trtr

n I clone the repo, I don't see that folder: > >hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr > > Lance > > Martin Čech wrote: > > > Hi Lance, > > it seems the whole .git/ folder got accidentally uploaded there and it > causes trouble. I recomme

Re: [galaxy-dev] automatic adding of a tab in a fastq header

Thank you very much for solving this Fabien, The PR with your fix has been created here: https://github.com/galaxyproject/galaxy/pull/1985 Martin On Mon, Mar 21, 2016 at 5:43 PM fmareuil wrote: > Hi Peter, > > I worked on it today and I found the reason of this bug. In

Re: [galaxy-dev] automatic adding of a tab in a fastq header

gt; I'm glad to see your suggested fix has already been applied to > the Galaxy repository so should be in the next stable release. > > Thank you! > > Peter > > (Also thank you Martin, Nicola, Dan, etc) > > > On Tue, Mar 22, 2016 at 8:43 PM, Martin Čech <mar...@bx.psu.ed

Re: [galaxy-dev] Galaxy Conference

Hello Scott, have you seen the schedule at https://gcc16.sched.org/ ? The trainings are all listed, described, and categorized there, it should help you decide what to attend. >From my experience in addition to scientists there are many admins and developers attending the conference so you

Re: [galaxy-dev] Tool shed tools, manual dep installation

Hi David, one thing that you might be missing is that the wrapper for the infosec-approved version might not exist yet (you would have to adapt the older shed-wrapped version if there were any relevant changes). But this largely depends on what software you want to use. Besides that your flow

Re: [galaxy-dev] Tool shed tools, manual dep installation

wrong though. > > Thanks, > > DT > > -- > David Trudgian Ph.D. > Computational Scientist, BioHPC > Lyda Hill Department of Bioinformatics > UT Southwestern Medical Center > Dallas, TX 75390-9039 > Tel: (214) 648-4833 > > From: Martin Čech [mailto:mar.

Re: [galaxy-dev] New galaxy parameter type

Hi Katherine, an example of a datatype addition can be seen in this PR: https://github.com/galaxyproject/galaxy/pull/2452 You need to define a class and teach it to sniff files of your defined type (with a doctest) and how to generate peek for the datatype's datasets in history. Let us know if

Re: [galaxy-dev] New galaxy parameter type

Katherine please disregard my answer, I probably misread your question. :) M. On Fri, Jul 15, 2016 at 3:05 PM Peter Cock wrote: > Did you mean parameter as in input field shown > to the user? Like a combobox or text field? > > Since this happened to come up earlier

[galaxy-dev] Fwd: New galaxy parameter type

forwarding to the list -- Forwarded message - From: Katherine Beaulieu <katherine.beaulieu...@gmail.com> Date: Fri, Jul 15, 2016 at 3:45 PM Subject: Re: [galaxy-dev] New galaxy parameter type To: Martin Čech <mar...@bx.psu.edu> Thanks Peter, I will look into that.

Re: [galaxy-dev] Writing test for dataset collection

Hi Cristel, for a start I please have a look at http://planemo.readthedocs.io/en/latest/writing_advanced.html#test-driven-development and let us know if you have further questions. The documentation regarding this is a still bit scarce, I am sorry. Martin On Mon, Jul 11, 2016 at 3:24 PM Cristel

Re: [galaxy-dev] showing progress on running tasks

Hi Ryan, This is a fairly complex problem because the length of the run depends most often on input size, job algorithms, and computational capacity all of which are quite difficult to estimate. We have discussed it before and one of the ways to approach this is to gather statistics from as many

Re: [galaxy-dev] showing progress on running tasks

the progress instead of Galaxy estimating that. > > If instance, if the tool know it has 5 stages, it can report back to > Galaxy 20,40,60,80,and 100 % complete. > > I know this is complex but could be a nice feature. > > Please excuse any typos -- Sent from my iPhone > > O

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

Peter: depot is something we plan on maintaining and providing as a service as long as Galaxy. The cargo-port we will also expand in future (eg to provide dynamic fallback at installation time. It is the right place to put your mira backups (and any other packages you care about in recipes).

Re: [galaxy-dev] Tools using Galaxy's Python library?

Hi folks, the two of the Galaxy-born libraries have sources at our GitHub: https://github.com/galaxyproject/gops https://github.com/galaxyproject/sequence_utils Any improvements or PyPI-readiness work are welcome. Best, Martin On Tue, Jan 31, 2017 at 7:08 AM Peter Cock

Re: [galaxy-dev] Last stable galaxy Release 16.10 or 17.01 ?

Hello, 16.10 is the latest release however release of 17.01 is imminent and will probably happen early next week. The release_17.01 branch is what usegalaxy.org runs for the past few weeks without any big issues. The choice is yours but updating to release_17.01 now is alright I think as along as

Re: [galaxy-dev] regarding tool dependencies

a system on > several popular Linux configurations would be greatly appreciated! At the > moment, I have abandoned the idea of setting up Galaxy in my lab, due to > time-consuming configuration problems... hopefully, we can re-try in the > future. > > Many thanks once more, >

Re: [galaxy-dev] ImportError and Project life cycle

Hi Matthias, what version of Galaxy are you running? The tool you have installed seems to support only new Galaxies that have Conda dependency resolution enabled. We are currently in the middle of the transition of the Galaxy's ecosystem to this new dependency manager so there are rough edges

Re: [galaxy-dev] regarding tool dependencies

Hello Nir, the tool publishing process looks like this: tools for Galaxy are contributed by developers like you to the Tool Shed https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some tools have dependencies,

Re: [galaxy-dev] Upgrade migration scripts

Hi Matthias, DB migrations need only to be run when there is a change in DB schema in between the releases. That is not the case between 16.10 and 17.01 so there is no migration to be run. When there is a migration to run, the startup process of Galaxy will abort and you will be presented with a

Re: [galaxy-dev] Can't downgrade database.

Makis, you need to run the downgrade command (sh manage_db.sh downgrade --version=129) from the folder with the newer Galaxy. The old one does not have the downgrading scripts. Thanks for using Galaxy. Martin On Tue, Jan 17, 2017 at 7:33 AM Makis Ladoukakis wrote: >

Re: [galaxy-dev] Shared Data Library, large number of files

Hi all, *Devon* is correct -the old data library UI under Admin menu is still in place (because it has some features perceived as important to some admins). However majority of users and most of the admins are using the interface under 'Shared Data' I hope and the old UI is deprecated since 15.10

Re: [galaxy-dev] Testtoolshed status

This has been fixed now, thanks Steve for the report and sorry for the trouble. Martin On Fri, Sep 2, 2016 at 10:20 AM Dave Bouvier wrote: > Steve, > > Thank you for reporting this issue, we've determined a potential cause > and are working to correct it. > > - > Dave Bouvier

Re: [galaxy-dev] error on startup

previous instance of reports running, and I'm not sure what to check as > far as ports. > our AWS guy said it might be an issue with AWS but I don't know enough > about all this to confirm (or to know how to confirm). > > thanks for your help. > > On Thu, Sep 1, 2016 at 1:39 PM,

Re: [galaxy-dev] error on startup

Hi Cris, what `host` and `port` is in your reports.ini config file? This stacktrace would point at something already running at the same port. Martin On Thu, Sep 1, 2016 at 12:36 PM Cristel Thomas wrote: > Galaxy admins, > One of you has probably seen the below error

Re: [galaxy-dev] error on startup

; this is the first time we have that issue though, and the instance has > been running just fine until now. I don't think we've changed anything. > > On Thu, Sep 1, 2016 at 12:40 PM, Martin Čech <mar...@bx.psu.edu> wrote: > >> Hi Cris, >> >> what `host` and `

Re: [galaxy-dev] delete user and all trace of user

Hi Edgar, there is no built-in way in Galaxy to remove a user completely. 'Deleting' just flips the flag in the DB and 'purging' is related to their data/histories. You need to access the DB directly if you want to completely remove a user. Beware that there might be constraints/relations

Re: [galaxy-dev] delete user and all trace of user

; *Edgar Fernandez* > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la Communication > > *Université de Montréal* > > > > PAVILLON ROGER-GAUDRY, bureau X-210 > > ( Bur. : *1-514-343-6111 poste 16568* > &g

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

Hello Stephanie, I have just tested this on 16.07 and on `dev` branch of Galaxy and it works for both in my case. Can you please check the browser's console for javascript errors? Thanks, Martin On Tue, Sep 13, 2016 at 10:22 AM Stephanie LE GRAS wrote: > Hi there (again), >

Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

for your feedback. We don’t have any javascript errors… > > > > Stephanie > > > > *De : *Martin Čech <mar...@bx.psu.edu> > *Date : *mardi 13 septembre 2016 16:36 > *À : *Stephanie Le Gras <sleg...@igbmc.fr>, " > galaxy-dev@lists.galaxyproject.org"

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

> > It’s 15.03. > > > > Regards, > > Dineli > > > > *From:* Martin Čech [mailto:mar...@bx.psu.edu] > *Sent:* Tuesday, September 13, 2016 10:31 PM > *To:* Amarathunga A. Dineli Karunath; galaxy-...@bx.psu.edu > *Subject:* Re: [galaxy-dev] Trimmomatic to

Re: [galaxy-dev] Trimmomatic tool is not visible in the workflow editor

Hi Dineli, what version of Galaxy do you have installed? thanks Martin On Tue, Sep 13, 2016 at 10:27 AM Amarathunga A. Dineli Karunath < dineli_karunathil...@nuhs.edu.sg> wrote: > Hi, > > I have a local galaxy instance and have installed many tools from the > galaxy tool shed. Recently I have

Re: [galaxy-dev] samtools

Hi Rui, you can install the following suite which includes about a dozen of wrapped samtools. https://toolshed.g2.bx.psu.edu/view/devteam/suite_samtools_1_2/5b673ccc8747 Martin On Mon, Sep 26, 2016 at 11:05 AM Beginner TI wrote: > I did see that if I click each

Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

Hi Rui, there is no 'mirror' button to obtain Main's toolset yet, but many pieces are in place to help you with this. Please see the following answers for guides and links: https://biostar.usegalaxy.org/p/11338/ https://biostar.usegalaxy.org/p/19660/ Thanks, Martin On Mon, Sep 26, 2016

Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

Hi Martin, > > Thanks! > > The first link doesn't really work...upon going to github it gave me 404. > After I explored a bit more > it says itself that it may not work now. :-( > > However the second one looks quite promising! > > Cheers, > Rui > > On Mon, Sep 26,

Re: [galaxy-dev] Help wanted: setting up a production server

Hi Steve, make sure to check out https://wiki.galaxyproject.org/Events There are 2 extensive admin trainings going to happen in near future. November in Salt Lake City and February in Melbourne. Martin On Fri, Oct 7, 2016 at 4:23 PM Steve Cassidy wrote: > Hi all, >

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