[galaxy-dev] Release of Galaxy 19.09

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 19.09. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/19.09_announce.html and user facing release notes are at

[galaxy-dev] Re: Galaxy jobs on Apache Mesos with chronos.py runner

Hi Pietro, Thanks for trying that runner! Some background here regarding the volume directory issue: https://github.com/galaxyproject/galaxy/pull/3946 https://github.com/galaxyproject/galaxy/pull/3946/files/2099c09f6ab5a8f5951d01cd6fa67681618e2dda#r112457231 It looks to be a known and

Re: [galaxy-dev] XMLs not reloading in all processes (UWSGI)?

Does your tool_conf.xml file have monitor="true" on the toolbox tag (e.g. - https://github.com/galaxyproject/galaxy/blob/dev/config/tool_conf.xml.sample#L2)? I guess the tool reload option will only work in a single process setup - but the monitoring with watchdog should be sufficient to not need

Re: [galaxy-dev] Job Script Integrity

Sorry for the late response. This generally means that Galaxy thinks a job script has been written and should be executable but the file system and operating system doesn't think the file is yet ready for execution. This could be for instance caused by NFS caching of file system permissions I

Re: [galaxy-dev] tool dependencies

On Thu, Nov 16, 2017 at 12:01 PM, Matthias Bernt wrote: > Hi all, > > I tried to install velvetoptimizer (for the assembly tutorial in the GTN). > > It lists velvetoptimiser as requirement in the main xml and the > tool_dependencies.xml (listing the installation steps). Now there

Re: [galaxy-dev] Galaxy moves files form job directory but attempts to look for them at original path

Well that is no good - I take it you have outputs_to_working_directory set to True in your galaxy.ini? That option doesn't get a lot of testing and it seems like it is interfering with retry_metadata_internally = True. What version of Galaxy are you running? Another work around would be to try to

Re: [galaxy-dev] broken after upgrade to 17.09 : uploading files via the API

Thanks for the report, I suspect the breaking change would be this - https://github.com/galaxyproject/galaxy/pull/4563. I added a bunch of tests for these API changes that I though would ensure backward compatibility but perhaps there is some sort of breakage here. I opened a PR in response to

Re: [galaxy-dev] Cron Job Tool

Unfortunately Galaxy has no native support for scheduled jobs or workflow executions like this. Pretty much all computation in Galaxy is kicked off by user action or external interaction via the API. So if you want to place the actual computation inside of Galaxy as a workflow or a tool you can -

Re: [galaxy-dev] resubmission on out of memory

Something like this is possible with some caveats. It is possible to detect memory and walltime errors - but not based on regex in tools but instead by the job runner. So the SLURM runner implements detection of out of memory errors and timeout I think - I don't think most of the other runners do.

Re: [galaxy-dev] numpy problem

On Tue, Aug 8, 2017 at 8:01 AM, Matthias Bernt wrote: > Dear dev-list, > > here an answer to my own question. > > The problem was that the tool "Group data by a column and perform aggregate > operation on other columns." returned an error: > > Traceback (most recent call last):

Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

There is an open issue for these paths not working with vanilla Galaxy tools https://github.com/galaxyproject/galaxy/issues/1676. -John On Wed, Aug 9, 2017 at 10:03 AM, Peter Cock wrote: > I'm puzzled now too, cross reference > >

Re: [galaxy-dev] inconsistent state set for workflow submissions [using bioblend]

The history state being 'ok' isn't a great metric for determining if the workflow is complete. The history state essentially only tells you if there are datasets of certain states in the history. At the start of the workflow - the invocation may be backgrounded and getting ready to run so there

Re: [galaxy-dev] Singularity Container forks ?

> hi, > > i have question when submitting jobs as real user > > defaults = "$galaxy_root:default_ro,$tool_directory:default_ro" > > singularity gives a WARNING since the home dir is already mounted > "WARNING: Not mounting requested bind point (already mounted in &

Re: [galaxy-dev] Singularity Container forks ?

Sorry for the late response - but earlier this week Björn Grüning and I added various support to Galaxy's development branch for Singularity. The following pull request added Singularity support in job running ( https://github.com/galaxyproject/galaxy/pull/4175) - here job destinations may

Re: [galaxy-dev] location of history id

(Once more with the list cc'ed - sorry for the duplicate message.) The IDs are encoded before they are shared out via the API so that raw integers aren't exposed. The ID the API returns is generally the value in the id column for that table. Eric Rasche kindly contributed a script to the

Re: [galaxy-dev] Galaxy Start Up Error - Double Requirements, Tempita

I've never seen anything like this - have you modified Galaxy's requirements.txt file or are you using the one that ships with Galaxy? On Fri, May 12, 2017 at 11:20 AM, Yip, Miu ki wrote: > Hi all, > > When attempting to start up Galaxy, via the run.sh script, we’re getting the >

Re: [galaxy-dev] Newline characters for txt files

Sorry for the delayed response on this - I just wanted to confirm that yes Galaxy does this for uploaded files (if tools produce these line endings we would not touch those). I believe this can be disabled by clicking on the settings icon for a particular upload row in the upload form and

Re: [galaxy-dev] View uploaded files

Do you have ``nginx_x_accel_redirect_base = /_x_accel_redirect`` set in your Galaxy ini file? Do you know what user nginx runs as? If yes, do you know if it has access to /home/galaxy/Software/galaxy/ database/files/000/dataset_140.dat? I'd su to become that nginx user and just make sure it can

Re: [galaxy-dev] All Jobs Error Out

Did you figure this out? It looks like you jobs are not detecting Galaxy's virtualenv and so they are getting a dependency (in this case mercurial) from Galaxy root packages. I'd review this document: https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers

Re: [galaxy-dev] Problem with installing tools using Conda

I've never seen anything like this before - I am sorry. Hopefully someone else will have a more concrete idea. Does that Conda executable work on the command line? I'd try removing the whole Conda folder and rebuilding it. Is it possible the install was corrupted at some point - maybe during

Re: [galaxy-dev] Relabeling dataset pairs in 'list:paired' collection

Thanks for your interest in this topic. The collection operations exist the way they do as tools distributed with the core framework because they can't be expressed as normal tools and they utilize abstractions that I don't consider public at this time (or really have any confidence in making

Re: [galaxy-dev] Configuring Galaxy, Pulsar and Conda

Hello, Thanks for working on this - Pulsar still hasn't quite caught up with Galaxy in terms of support for Conda but we are getting there. So I noticed two things that should help today when I was trying to recreate your problem - the first is that Conda support in Pulsar requires this PR

Re: [galaxy-dev] Pulsar Metadata

I perhaps don't understand the question. As long as the "datasets" are Galaxy datasets and they appear in the command-line specific by the "command" block of your tool - it should be transmitted. When you say a "dataset list of files" - do you mean (1) a Galaxy collection, (2) a set of files

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

So the PR that broke your tools is probably here https://github.com/ galaxyproject/galaxy/pull/3364/files. That pull request removed Galaxy from the Python path of Galaxy tools - this gives tools a much cleaner environment and prevents certain conflicts between Conda and Galaxy. As part of that

Re: [galaxy-dev] Problem with 'galaxy_packages' dependency resolver in versionless mode

I recently reworked the dependency resolver documentation and made this explicit. I don't think the previous revision of that document mentioned this important caveat at all. Thanks for Galaxy-ing! Thanks, -John On Tue, Jan 24, 2017 at 7:01 AM, Peter Briggs wrote:

Re: [galaxy-dev] Making symlinks in "command" section of tool XML

At first glace I think the problem is that when you use the ``interpreter`` tag Galaxy has really broken logic for modifying the command line to use that. ln works just like cp and mv. Those too would be broken for this tool because of the interpreter attribute I think. For this reason

Re: [galaxy-dev] psycopg2 module and SSL connection to postgresql

I don't know what the particular issue is - I do know that after a lot of trial and error we were able to get Postgres + SSL working at MSI before I left my previous job there - so there is hope. I will say however, upgrading even to one newer Galaxy - namely 16.01 might solve this issue. We

Re: [galaxy-dev] Pulsar - running as real DRMAA user problems

Glad this almost worked - I'm not sure what the problem is. I'd open the file /cluster/galaxy/pulsar/pulsar/managers/util/drmaa/__init__.py - and add some logging right before this line - (return self.session.jobStatus(str(external_job_id))). log.info("Fetching job status for %s" %

Re: [galaxy-dev] Job_id in a galaxy tool

Can you clarify this? Do you want access to the job id during the job execution or do you want to see it after the job is complete? It is currently available after the job is complete using the "i" (view details) button. If you want access to the job id as part of the tool execution that is

Re: [galaxy-dev] Local galaxy samtools HISAT 2 issue

I think this is caused because Galaxy needs to have samtools available on its PATH. Is this an older version of Galaxy? I feel like newer versions maybe make this error more clear. Hope this helps - hopefully very quickly here we solve this problem by switching to pysam for these operations so an

Re: [galaxy-dev] Tool wrapper NotFound error

It looks like your library conditional is wrapped in a section called "basicOptions". For this reason when it appears in your block you need to use $basicOptions.library.type for instance instead of $library.type. Hope this helps and thanks for using Galaxy! -John On Wed, Oct 26, 2016 at 11:39

Re: [galaxy-dev] Workflow ID, Galaxy Instance URL, API Key in Galaxy Tool Config

In general we discourage this - but there is some conversation about this here - at least as it pertains to the instance URL and API key: http://dev.list.galaxyproject.org/find-UUID-of-current-history-in-tool-XML-wrapper-td4667113.html The workflow is more tricky - if you are sure the job is

Re: [galaxy-dev] Galaxy Feature Request: Input naming deficiencies

Hello Zipho, Per your request I have reviewed the linked issues and created a list of things I think can be done that are relatively easy to improve the current situation here https://github.com/galaxyproject/galaxy/issues/2980#issuecomment-250777589. There are a lot bigger things that need to

Re: [galaxy-dev] Problem with conda on galaxy 16.07

Any follow up on this? I have never seen this - but it would be worth specifying a full absolute path for conda_prefix in galaxy.ini and see if that fixes it. If it does - I can open a PR that makes sure this variable is always an absolute path. On Thu, Sep 1, 2016 at 11:37 PM, Léo Biscassi

Re: [galaxy-dev] why modified workflow doesn't save?

This usually means there is an error of some kind - perhaps a missing tool. Sorry it is not more transparent - I'd check the Galaxy logs for an error message if possible or open the JavaScript console of your web browser

Re: [galaxy-dev] Consuming dataset collections

to a bunch of things that are opaque to a separate > script. Would it be a useful goal to have a richer galaxy-tool interface that > could make all information available to the tool wrapper visible to my Python > script? One way to do that would just be to bundle everything up in JSON

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

Yup - thanks for the bug report. I have used your rna example to build a minimal-ish example to fit into Galaxy's test tools framework here https://github.com/galaxyproject/galaxy/pull/2795. I also tested in 16.01 and it worked - so this clearly broke in 16.04. I'll see if I can track it down and

Re: [galaxy-dev] uploading multi-file archives and creation of potentially large collections

Just to provide a little more detail on the collection point... Daniel Blankenberg presented a talk at the Galaxy Community Conference on metagenomics that talked a lot about "large" collection handling in Galaxy - https://gcc16.sched.org/event/5Y0M/metagenomics-with-galaxy. I think his rule of

Re: [galaxy-dev] Consuming dataset collections

Thanks for the questions - I have tried to revise the planemo docs to be more explicit about what collection identifiers are and where they come from (https://github.com/galaxyproject/planemo/commit/a811e652f23d31682f862f858dc792c1ef5a99ce).

Re: [galaxy-dev] cannot extract genomic dna

- It needs to be a tab not spaces between the fields in that loc file - can you confirm that it is a tab? (Many editors will implicitly replace tabs with spaces.) - You need to restart Galaxy after updating that file - can you confirm it has been restarted? -John On Fri, Jul 22, 2016 at 11:34

Re: [galaxy-dev] switching from Apache to "auth_conf" to handle external user authentication via LDAP

I can't confirm it is going to work without negative repercussions - I can only say that I cannot think of any non-obvious problems that would result from doing this. It seems like it is going to be the right thing to do in your case (but no promises :)). If it works, it would be super awesome if

Re: [galaxy-dev] Using session parameters in Galaxy tools

This information is not readily accessible during tool command line generation. You can access some extra data with the $__user__ object - it is the underlying model object. Are you hacking the session information with extras or do you want stuff already associated with the Galaxy session such as

Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

I think newer versions of Galaxy give a better error message - I am pretty sure the problem is you are missing samtools. It needs to be available on the PATH for Galaxy if you use bam data. -John On Fri, Jun 3, 2016 at 1:00 PM, Anthony Underwood wrote: > > > Jobs

Re: [galaxy-dev] Refresh of screens in Galaxy Docker environment

It is probably worth looking at this Galaxy issue - this may have little to do with Docker or the Docker server might have a different time configured than a local one? History updating is broken for many clients in 16.04 and I am unsure if this intention is to fix it or not.

Re: [galaxy-dev] Changing temporary directory for planemo

Resending because I forgot to reply-all: Older versions of Planemo should just respect an 'export TMPDIR="/new/tmp"' before calling planemo. I think recently we introduced a work around for some conda problems (https://github.com/galaxyproject/planemo/pull/460) that causes this not to be

Re: [galaxy-dev] Planemo inside of Conda

Galaxy and Planemo cannot co-exist in the same conda environment I don't think - because planemo requires galaxy-lib (https://github.com/galaxyproject/galaxy-lib) which cannot be installed in Galaxy's environment. I don't understand the intricacies of what you are trying to do or why it worked in

Re: [galaxy-dev] Problem with DRMAA and Pbs Pro

Thanks for the report and the workaround. I have opened a Pull Request to make this truncation the default behavior in Galaxy 16.04. https://github.com/galaxyproject/galaxy/pull/2265 -John On Thu, Apr 28, 2016 at 5:43 AM, Tiziano Flati wrote: > Solved. > > For your

Re: [galaxy-dev] Planemo test with SGE

Did you ever figure this out? I cannot think of anything that would cause this - if the job conf is working with Galaxy it should work with planemo. Are you sure Galaxy was actually using the configuration and not just the local runner. Is it possible you've modified run.sh to modify the

Re: [galaxy-dev] per-tool job resource defaults

This mapping is not automatic - you need to write a small Python method to take these parameters specified by the user and map them to your cluster parameters. These methods are called dynamic job destinations and described on the wiki at:

Re: [galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

Yeah - your discoveries are exactly right. 16.04 has added the ability to configure a bunch of extra things on a per-job-destination basis but this isn't included yet - probably should be though. Pulsar would be a way to go - hopefully soon Pulsar will be included with Galaxy directly and it will

Re: [galaxy-dev] Job stuck in running state.

What kind of database backend are you using (postgres, myql, or the default sqlite)? If you are running many jobs - I would definitely encourage using postgres. -John On Sun, Mar 13, 2016 at 2:48 PM, Zuzanna K. Filutowska wrote: > Dear All, > > I am running newest

Re: [galaxy-dev] Problems uploading files to galaxy

If you are running jobs as "the real user" with drmaa (using the chown script) - you will probably want to setup a separate job destination using the local runner for upload jobs. The upload tool uses files that are created outside of Galaxy and these aren't modeled well. Does this help? -John

Re: [galaxy-dev] workflows "show in menu" by default

There is no option to enable this automatically. There is not ability to modify this via the API (though I created an issue here https://github.com/galaxyproject/galaxy/issues/1842). I guess what I would do to implement this is to refactor places where trans.user.stored_workflow_menu_entries is

Re: [galaxy-dev] Load tools without service interruption

Hans is correct prior to Galaxy 16.01. The 16.01 release of Galaxy added a monitor attribute to config/tool_conf.xml.sample (e.g. ) that causes Galaxy to watch that file for changes and reload the toolbox on modifications. No need to add this to tool shed tool confs (and it would probably break

Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

Forgot to cc the mailing list. -John On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchil...@gmail.com> wrote: > Are you sure about the --file when calling Rscript? > > Here is the usage for my local version which does not expect an > argument named --file: > > Usage: /pa

Re: [galaxy-dev] Galaxy sending jobs to multiple clusters

Nate has a branch of slurm drmaa that allows specifying a --clusters argument in the native specification this can be used to target multiple hosts. More information can be found here: https://github.com/natefoo/slurm-drmaa Here is how Nate uses it to configure usegalaxy.org:

Re: [galaxy-dev] Running Galaxy jobs remotely via ssh / rsh

stalled this as root in > /root/torque-6.0.0.1-1449528029_21cc3d8 > > Thanks! > > On Wed, Jan 20, 2016 at 12:27 PM, John Chilton <jmchil...@gmail.com> wrote: >> >> Even if you just have two servers, I would strongly recommend you >> setup a cluster

Re: [galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 3:26 PM, Peter Cock wrote: > On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock > wrote: >> Hello all, >> >> We're currently looking at changing our Galaxy setup to link user accounts >> with Linux user accounts for better

Re: [galaxy-dev] Creating cluster_files_directory (default database/pbs)

Peter - Nate and I are in agreement that the goal is to eliminate that directory, so I don't want to put effort into automating its creation. https://github.com/galaxyproject/galaxy/issues/1576 If you wish to open a PR that does this though, I would be happy to merge this. The best place to

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

On Mon, Jan 25, 2016 at 3:44 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Thanks John, > > On Mon, Jan 25, 2016 at 3:29 PM, John Chilton <jmchil...@gmail.com> wrote: >> The script generated to call Galaxy is here: >> >> https://github.com/galaxyproje

Re: [galaxy-dev] Data Collection collection_type list:list

list:list (as well as list:list:paired, list:list:list, etc...) can be created via the API or using tools. As an example of the second - if you had a tool that took in a dataset and split it into a list and then mapped a list over that tool - Galaxy would produce a list:list output from the

Re: [galaxy-dev] Running Galaxy jobs remotely via ssh / rsh

Even if you just have two servers, I would strongly recommend you setup a cluster distributed resource manager (DRM) like SLURM, PBS, or Condor and ensuring there exists a shared file system between Galaxy and the node running the jobs. You wouldn't even need to use the CLI job runner - you could

Re: [galaxy-dev] Some workflows not scheduled until handler restart

I've been swamped with release related things but my intention is to dig deeply into this. This is a very serious bug. A work around is just to disable beta workflow scheduling for now: switch force_beta_workflow_scheduled_min_steps=1 force_beta_workflow_scheduled_for_collections=True to

Re: [galaxy-dev] This job is waiting to run - Issue after Update to 15.10

We have heard no other reports of this and I have not replicated it locally, is it possible this was like a client-side caching error or something that went away? If not, can you retry updating to the latest commit of release_15.10 - there have been a good number of bug fixes though I don't

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

I would review the following threads - they have hacks for doing this and required warnings: http://dev.list.galaxyproject.org/find-UUID-of-current-history-in-tool-XML-wrapper-td4667113.html http://dev.list.galaxyproject.org/Possible-to-pass-hostName-to-a-tool-td4667108.html -John On Sun, Dec

Re: [galaxy-dev] IE setup problem

dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to False and use supervisord if you have any inclination to at all. Like sqlite or the local job runner, it is just an attempt to make sure things work out of the box but it isn't that robust. -John On Sat, Dec 19, 2015 at 1:20

Re: [galaxy-dev] unexpanded macros

Hey Brad, What version of Galaxy are you on? Parameterized macros are pretty new and will not work on older Galaxies. -John On Fri, Dec 4, 2015 at 3:36 AM, Langhorst, Brad wrote: > Hi: > I just installed hisat2 and the data manager from the toolshed …. > > Some macros seem

Re: [galaxy-dev] AssertionError: ID tag is required for a Display Application

Despite sounding very similar, visualizations and display applications are different things - display applications for the most part send or expose Galaxy data to outside sources, visualizations run on the Galaxy server and the client side. It seems like you are trying to configure a

Re: [galaxy-dev] unexpanded macros

Yeah - those wrappers are not going to work with 15.05. Parameterized XML macros were added in 15.07 it looks like (http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html). -John On Thu, Dec 10, 2015 at 10:28 PM, Langhorst, Brad wrote: > Hi: > > I’m at

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

Someone should create an tools-iuc issue for this, I will certainly participate also. I don't know anything RADSeq (or really much about any kind of Seq) but I suspect I can find a way to help if there is a TODO or ideas list that is tracked on github. Thanks all, -John On Mon, Nov 23, 2015 at

Re: [galaxy-dev] workflow API: step_order vs step_id in bioblend

s John, I found indeed the step order ids in the result from > export_workflow_json. Helps a lot and now I won’t need to use soon-deprecated > stuff. > > cheers, > — > Jorrit Boekel > Proteomics systems developer > BILS / Lehtiö lab > Scilifelab Stockholm, Sweden > > &

Re: [galaxy-dev] Planemo 0.20.0 and xunit

via pip, hmm... -John On Fri, Nov 20, 2015 at 12:58 AM, Tiago Antao <t...@popgen.net> wrote: > On Thu, 19 Nov 2015 20:35:42 +0000 > John Chilton <jmchil...@gmail.com> wrote: > >> The latest development release of Galaxy which planemo targets by >> default require

Re: [galaxy-dev] Unable to up Planemo against latest dev

> NoseTestDiff-0.1-py2.7.egg > > Christian > > From: Peter Cock [p.j.a.c...@googlemail.com] > Sent: Friday, November 20, 2015 12:41 PM > To: Christian Brenninkmeijer > Cc: John Chilton; galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-dev] U

Re: [galaxy-dev] Planemo 0.20.0 and xunit

On Tue, Nov 17, 2015 at 8:21 PM, Tiago Antao <t...@popgen.net> wrote: > On Tue, 17 Nov 2015 14:48:03 +0000 > John Chilton <jmchil...@gmail.com> wrote: > >> Thanks for the bug report. Somehow Galaxy isn't installing the >> development wheels into the transient Galaxy's

Re: [galaxy-dev] workflow API: step_order vs step_id in bioblend

The workflow API is the only place where we expose unencoded IDs and we really shouldn't be doing it. I would instead focus on adapting to using step_ids - they really should be more stable and usable. Order index has lots of advantages - You can build a request for a given workflow and apply it

Re: [galaxy-dev] Planemo 0.20.0 and xunit

Thanks for the bug report. Somehow Galaxy isn't installing the development wheels into the transient Galaxy's virtualenv, I've wiped out my planemo caches and I can't reproduce this locally. Can you send me the green log messages at the beginning of the test command as well as the few lines after

Re: [galaxy-dev] galaxy folder tree permissions

installed tools and their deps? > > -- > David Trudgian Ph.D. > Computational Scientist, BioHPC > UT Southwestern Medical Center > Dallas, TX 75390-9039 > Tel: (214) 648-4833 > > Please contact biohpc-help@utsouthwestern with general BioHPC inquries. > > -----Original M

Re: [galaxy-dev] list collection output - format set from input

d, but no success. >> Code: >> >>> >>> >>> >> directory="output" /> >>> >> >> >> It puts the samples into the collection correctly, but doesn't set a data >> type. >> >> Weird enough: In t

Re: [galaxy-dev] Tool code for symlinking a data collection from input to output?

on building up workflows from YAML can be found at https://github.com/galaxyproject/galaxy/pull/1096 and https://github.com/galaxyproject/bioblend/pull/143. -John On Tue, Nov 17, 2015 at 7:24 PM, Eric Rasche <e...@tamu.edu> wrote: > > On 11/17/2015 01:18 PM, John Chilton wrote: >> The

Re: [galaxy-dev] Tool code for symlinking a data collection from input to output?

Slowly trying to catch up on e-mail after a lot of travel in November and I answered a variant of this to Damion directly, the most relevant snippet was: " I would not symbolic link the files though. I would just take the original collection and pipe it into the next tool and add a dummy input to

Re: [galaxy-dev] Opening Galaxy with a specified History Name -- how to convert the clear text history id to an encrypted id?

> How does one obtain that, or convert the clear text version to an encrypted > id? > > Thanks again, > > Bob > > - Forwarded Message - > From: John Chilton <jmchil...@gmail.com> > Cc: galaxy-dev@lists.galaxyproject.org > Sent: Mon, 14 Sep 2015 13:44:01 - (UTC)

Re: [galaxy-dev] Workflow 'Input Dataset' Ressolution Issue

Albuquerque <marcoalbuquerque@gmail.com> wrote: > So in other words, there is no release that I can update my cloudman > instance to? > > Marco > > On Sun, Oct 11, 2015 at 3:49 PM, John Chilton <jmchil...@gmail.com> wrote: >> >> Yeah - release_15.07 i

Re: [galaxy-dev] Get the working directory within the ncbi_blastp_wrapper.xml file

I'd keep working on pbs_python or switch to drmaa that frequently works for the same distribution. There is also a CLI runner that just executes qsub and qstat commands directly on the localhost or can also ssh into a remote host and execute these commands.

Re: [galaxy-dev] Workflow 'Input Dataset' Ressolution Issue

90501d2d9. > > Is there maybe a different revision I should be using? > > Marco > > On Sun, Oct 11, 2015 at 11:03 AM, John Chilton <jmchil...@gmail.com> wrote: >> >> This sounds like it corresponds to this issue >> https://github.com/galaxyproject/galaxy/issues/776. Is

Re: [galaxy-dev] Some issues with job submission to pulsar

Depending on how you set things up - either Galaxy, Nginx, or Apache are creating a file for the upload that is incoming - in the above case I imagine it is this file - /home/galaxy/wkdir/galaxy/database/tmp/tmpp6j83l. This file is outside of Galaxy's data model for tools and jobs - it is just a

Re: [galaxy-dev] validator type="empty_field" is not working within repeat tags

Thanks for the bug report. This has been fixed by Dan with PR 798 for version 15.07 if you deploy Galaxy via Git. https://github.com/galaxyproject/galaxy/pull/798 -John On Mon, Jun 1, 2015 at 9:17 AM, Anmol Hemrom wrote: > Hi, > > I was trying to enforce not to allow empty

[galaxy-dev] Galaxy Tools and Collections Remote Hackathon (Thursday and Friday)

Hello All, This is just a reminder that the Galaxy Tools and Collections Remote Hackathon will be tomorrow Thursday the 17th and Friday the 18th of September. More details can be found at: https://github.com/galaxyproject/tools-iuc/issues/239 This Github issue includes a big list of potential

Re: [galaxy-dev] Subtleties of and escaping dollar signs

gt; > I like that plan - is the XSD at the point where we can declare > it in Galaxy Tool definition XML files s & validate them (via > planemo or otherwise)? > > Peter > > On Wed, Sep 9, 2015 at 7:03 PM, John Chilton <jmchil...@gmail.com> wrote: >>

Re: [galaxy-dev] Opening Galaxy with a specified History Name

Thanks, > Bob > - Original Message - > From: John Chilton <jmchil...@gmail.com> > To: rbrown1...@comcast.net > Cc: galaxy-dev@lists.galaxyproject.org > Sent: Wed, 09 Sep 2015 15:32:39 - (UTC) > Subject: Re: [galaxy-dev] Opening Galaxy with a specified History Nam

Re: [galaxy-dev] discover_datasets

Just reran this tool and it did indeed give me multiple outputs. I think the problem is the files appear but the history needs to be refreshed to see them. There is a little refresh icon at the top of the history panel that is needed. This is a known limitation of the multiple file output support

Re: [galaxy-dev] planemo and tool dependencies

Thanks again for implementing this Christian and for outlining how to maybe use it for testing. I'll try to add some support and documentation to planemo for how to use it - https://github.com/galaxyproject/planemo/issues/290 - it is not my favorite long term 100% solution to this problem - but it

Re: [galaxy-dev] Subtleties of and escaping dollar signs

Updated the wiki with this information. https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cversion_command.3E_tag_set. We got to get away from using the wiki page and start documenting this stuff in the XSD (https://github.com/JeanFred/Galaxy-XSD) directly and build the documentation

Re: [galaxy-dev] BUG: Collections and History export

Thanks for the report, this is a sort known issue (https://trello.com/c/WodW2sLb, https://wiki.galaxyproject.org/Develop/GSOC/2015Ideas#Easier_or_More_Robust_History_Imports_and_Exports). I think at some point someone on the team will need to take some time to work on history import and export, it

Re: [galaxy-dev] login problems when using a proxy and serving at a subdirectory

Not really sure what is happening here, does your galaxy.ini file have the following sections: [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy If yes, it might be best to share nginx configuration and your galaxy

Re: [galaxy-dev] Galaxy and PBS/Torque Cluster

Ryan, Not sure what the problem is. I'm not sure the Galaxy that is distributed with Biolinux is really setup to be used with PBS/Torque. If you have pbs/torque installed and running properly and if you can submit job scripts via the qsub command as whatever user Galaxy runs under - the

Re: [galaxy-dev] samtools dependency changes ?

So it wasn't in 15.01 - it was before that but the local job runner was changed to set metadata as part of the job (I think probably sometime in 2014). When it was setting metadata externally it might have used slightly different dependency resolution strategies that would result in samtools being

Re: [galaxy-dev] Rename output from a repeat

I don't think there is a way given the implementation. The name of the association is repeatname_0|input1 but the | is treated as a special symbol so it won't be used to get the parameter. I have opened a PR to allow this: https://github.com/galaxyproject/galaxy/pull/662 The syntax in the

Re: [galaxy-dev] Dataset Collections status

On Fri, Aug 7, 2015 at 8:01 PM, Keith Suderman suder...@cs.vassar.edu wrote: Greetings, I started pulling Galaxy code from the dev branch a few months ago to take advantage of the (then just emerging) dataset collections feature. However, it is not clear to me from the latest release notes

Re: [galaxy-dev] migrated_tools_conf.xml propose

My understanding is a bit limited but I believe the file is used to track tool shed installed tools that use to belong in the Galaxy distribution. I don't think it has much use for a new Galaxy instance and no - I don't believe there is a way from the command-line to sort of synchronize this file

Re: [galaxy-dev] IOError kills collections

Are you running jobs on the head node or just Galaxy? If this is a consistent problem and you are running jobs on the head ndoe I would disable that. As to resume just the failed jobs - this is not currently possible but really should be ideally. https://trello.com/c/lxVJy7fs -John On Mon, Jul

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