[galaxy-dev] planemo and tool dependencies

Hi all, I'm trying to test some tools under planemo and can't find out how to have it install tool dependencies while setting up the environment. The dependency is on a particular python module and we have a tool_dependencies.xml file to describe it. I can't see a way to tell planemo serve etc t

Re: [galaxy-dev] planemo and tool dependencies

versity of Manchester > -- > *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf > of Steve Cassidy [steve.cass...@mq.edu.au] > *Sent:* Thursday, September 03, 2015 9:00 AM > *To:* galaxy-dev@lists.galaxyproject.org > *Subject:*

Re: [galaxy-dev] planemo and tool dependencies

ackages DEBUG 2015-09-04 20:55:32,054 Unable to find dependency,'python_nltk_tools' '1.0' 'package' galaxy.tools.deps WARNING 2015-09-04 20:55:32,054 Failed to resolve dependency on 'python_nltk_tools', ignoring Thanks, Steve > Christian > ---

Re: [galaxy-dev] planemo and tool dependencies

umps and says there is another way! > > Christian > > PS. Either uses the testtoolshed or start your own. > > -- > *From:* Steve Cassidy [steve.cass...@mq.edu.au] > *Sent:* Friday, September 04, 2015 12:29 PM > > *To:* Christian Brenninkmeijer > *C

[galaxy-dev] Tools that make datasets

Hi all, I'm trying to understand how to write a tool that generates a dataset rather than a single output file. I've tried following all of the examples but I'm stuck, so I thought I would distil down the simplest example I could write and ask for help here. So here's my example: https://gist.

Re: [galaxy-dev] Tools that make datasets

ections/ > > On 20 October 2015 at 08:48, Steve Cassidy > wrote: > >> Hi all, >> I'm trying to understand how to write a tool that generates a dataset >> rather than a single output file. I've tried following all of the examples >> but I'm stuc

Re: [galaxy-dev] Tools that make datasets

> notice is the "directory" argument. If you write jobs to the current > directory instead of "output_path" can you get it to work? > > Peter > > On 20 October 2015 at 09:52, Steve Cassidy > wrote: > >> Thanks Peter, >> I did see that proviso somewher

Re: [galaxy-dev] Tools that make datasets

tory. > > So if you use: > > > > (note the < and > - this is effectively the regexp > r"(?P.*)\.txt" with the < and > escaped out) > > And alter the code so that it just writes files to the current directory, > then you'll pic

Re: [galaxy-dev] Tools that make datasets

ists else name > name means name > dbkey means dbkey > ext means ext > visible means visible > > > On 21 October 2015 at 08:44, Steve Cassidy > wrote: > >> Thanks, yes that works, though I'm not really sure what the difference is >> between __name__

[galaxy-dev] Position Vacant - Galaxy and Language Research in Sydney

Hi all, I’d like to draw your attention to the following vacancy on our project in Sydney, Australia: https://goo.gl/6NcY3g This is on the Alveo project and I’m posting here because part of the platform is a Galaxy server with tools developed to work on language data (text and speech). The

[galaxy-dev] planemo shed_create bug? on planemo/server docker image

I’m just getting my head around tool dependencies and in doing so trying to push my tools to a local toolshed which I can handily run with the planemo/server docker image via Kitematic. That toolshed is set up with an admin user plan...@test.com so I have a stanza in my

Re: [galaxy-dev] planemo shed_create bug? on planemo/server docker image

n or follow the > description on https://github.com/bioconda/bioconda-recipes to create a > PR and a package for your tool. > > This can be used by Galaxy automatically. > Thanks, > Bjoern > > Am 14.07.2016 um 03:49 schrieb Steve Cassidy: >> I’m just getting my head aroun

[galaxy-dev] Papers that cite Galaxy workflows

Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in the Bio field that cite Galaxy workflows. Even better would be the re-use of a Galaxy workflow cited in another paper. Does anyone have any good

[galaxy-dev] Consuming dataset collections

Hi all, I’m staring at the discussion of handling dataset collections: http://planemo.readthedocs.io/en/latest/_writing_collections.html but failing to see the solution to my problem. I have a tool that creates a dataset collection, a group of files with names like 1_1308_1_2_092-ch6-speaker

Re: [galaxy-dev] Papers that cite Galaxy workflows

pipeline defined in it. Hope this helps, Dave C On Thu, Jul 21, 2016 at 7:21 PM, Steve Cassidy mailto:steve.cass...@mq.edu.au>> wrote: Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in t

Re: [galaxy-dev] Consuming dataset collections

ith and > thinking about collections from inside some sort of script should have > the option to consume and produce manifests of files. > > I've created an issue for this idea here - > https://github.com/galaxyproject/galaxy/issues/2658. I'm not sure if > I'll have

[galaxy-dev] Storing data in the user session

Hi again, I’m looking for the right way to store some user credentials in the galaxy session so that tools can work on behalf of the user with our repository. Currently users have an API key and they need to upload it as a data item to that is then passed to each tool that needs it as input.

Re: [galaxy-dev] Storing data in the user session

be handled on the > framework level. > > Hope you are fine, > Bjoern > > Am 28.07.2016 um 03:15 schrieb Steve Cassidy: >> Hi again, >> I’m looking for the right way to store some user credentials in the >> galaxy session so that tools can work on behalf of the user w

Re: [galaxy-dev] Storing data in the user session

2016-07-28 9:42 GMT+02:00 Steve Cassidy mailto:steve.cass...@mq.edu.au>>: Hi Bjorn, sure, I don’t want to have the credentials stored in the tool but the tool needs to act on behalf of the user to retrieve data from the repository, so it needs access to credentials. This could for example b

Re: [galaxy-dev] Storing data in the user session

l. The only thing is missing the tag password on the xml then you can encrypt the password. I tried to add the new paramter on the build.py but I have some errors, don't know if someone arrived to fixed it. Mohamed 2016-07-28 10:00 GMT+02:00 Steve Cassidy mailto:steve.cass...@mq.edu.au>

[galaxy-dev] Putting it all together - toolshed tool + conda dependency

Hi all, I’m making baby steps towards having a repeatable installation for my tools. But I’m now stuck, so help would be appreciated. I have a tool that works and is in the test toolshed (alveoimport in Data Sources). It depends on my python package which is now part of bioconda (pyalveo, ve

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

//github.com/gregvonkuster/docker-galaxy-csg/blob/master/Dockerfile#L9 > > Hope this helps, > Bjoern > > Am 25.08.2016 um 12:32 schrieb Steve Cassidy: >> Hi all, >> I’m making baby steps towards having a repeatable installation for my >> tools. But I’m now stuck,

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

ND_ISOLATION anywhere other than in sample Dockerfiles - is this some kind of magic incantation that creates a rift in space-time…enquiring minds want to know!!! Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy > On 25 Aug 2016, at 9:54 PM, Steve Ca

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Python > environment (that's why sqlalachemy couldn't be found). > > Can you try updating the container or building from the dev branch? I think > the necessary changes for conda should be in the dev branch, which you can > pull with docker pull quay.io/bgruening/galaxy:dev.

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Looks like I’m hitting this issue: https://github.com/galaxyproject/galaxy/issues/2797 Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy > On 29 Aug 2016, at 11:09 AM, Steve Cassidy wrote: > > Thanks Marius, > I tried a build based on t

[galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

Hi, trying to get my tools going, part 29. I have a Docker image with the latest Galaxy release, patched to fix the Conda install bug I found earlier, my tools are installed ok and I’ve added a few from the toolshed for good measure. One of my tools requires R 3.0.2 which is installed ok. I

[galaxy-dev] Testtoolshed status

I’m getting a 500 response from the testtoolshed when I try to upload a tool via planemo: ➜ alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target testtoolshed apitools cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse HEAD cd '/Users/steve/projects/alveo-gala

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

Hi all, I’m working on setting up a Galaxy server for use with speech and language data. While I can probably get there myself eventually, I’m thinking it would be good to get some (paid) help if it were available. If you have some experience setting up a public facing Galaxy instance, and yo

Re: [galaxy-dev] Storing data in the user session

you should not populate a tool with credentials, this should be handled on the framework level. Hope you are fine, Bjoern Am 28.07.2016 um 03:15 schrieb Steve Cassidy: Hi again, I’m looking for the right way to store some user credentials in the galaxy session so that tools can work on behalf of th

Re: [galaxy-dev] Storing data in the user session

e more luck than me. http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104 Cheers, Katherine On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy mailto:steve.cass...@mq.edu.au>> wrote: Hi Bjoern, just wanting to revisit this quest

Re: [galaxy-dev] Storing data in the user session

e have in mind. Cheers, Bjoern Am 17.10.2016 um 23:31 schrieb Katherine Beaulieu: Ah I see, we had a similar problem except our service used a password and username so we ended up implementing a password parameter that didn't persist in the database. On Mon, Oct 17, 2016 at 5:29 PM, St

[galaxy-dev] Tool needs a particular file extension

Hi, I’m wrapping a tool that needs it’s input to have a known file extension (an audio file, eg. .wav). Since Galaxy stores all data as .dat files the tool is falling over since it doesn’t know what .dat is. I thought I’d be able to get around this by hard linking the .dat file to the same na

Re: [galaxy-dev] Tool needs a particular file extension -- now Datatype help

over 400 soft link examples: $ grep "ln -s" tools/*/*.xml | wc -l 446 Peter On Fri, Oct 21, 2016 at 5:48 PM, Steve Cassidy wrote: Hi, I’m wrapping a tool that needs it’s input to have a known file extension (an audio file, eg. .wav). Since Galaxy stores all data as .dat files the t

[galaxy-dev] planemo with --docker and --conda_dependency_resolution

Hi, I’m trying to test a few tools, one of which uses a docker container, the others use dependencies that can be found in conda. I can test each one by using either —docker or —conda_dependency_resolution with planemo, but when I try to give both of these, it seems to want to only use docker

Re: [galaxy-dev] Dynamic Tool UI based on script

Hi all, this would help in a tool I’m trying to write too but the problem I have implementing this approach is that my script will need an external python module - is there any way that I can list dependencies for the script? As it happens these are the same dependancies that the tool itself

Re: [galaxy-dev] Dynamic Tool UI based on script

-Rudolf Hotz mailto:h...@fmi.ch>> wrote: Hi Steve what happened, when you add this module to the environment the galaxy server is running in? (e.g. by listing the path in the 'run.sh' file) Regards, Hans-Rudolf On 12/07/2017 03:05 AM, Steve Cassidy wrote: Hi all, this would he

Re: [galaxy-dev] Dynamic Tool UI based on script

owever, tools relying on "dynamic_options" and extra "code" scripts are usually 'hacks' for accessing external data/services in a local galaxy installation. And such tools are not intended for the toolshed anywayIMHO. Hans-Rudolf On 12/07/2017 09:37 AM, Steve C