Re: [galaxy-dev] This job is waiting to run

2015-02-06 Thread Ryan G
. If this isn't working - there maybe a problem in your galaxy.ini file - I would need to know what properties were being set in there to know more though. -John On Mon, Feb 2, 2015 at 12:53 PM, Ryan G ngsbioinformat...@gmail.com wrote: I tried setting up Galaxy to use Sun Grid Engine

Re: [galaxy-dev] Tools to download SRA datasets from GEO

2015-02-05 Thread Ryan G
is part of the installation. Also, have you looked at the toolshed? e.g. https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit Regards, Hans-Rudolf On 02/04/2015 04:44 PM, Ryan G wrote: Do any tools exist to download GEO datasets from NCBI

[galaxy-dev] Manually adding new tools from toolshed

2015-01-15 Thread Ryan G
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes. Along with the new data types is

[galaxy-dev] Manually installing rsem_datatypes package from toolshed

2015-01-21 Thread Ryan G
I'm trying to manually install rsem_datatypes package into my local Galaxy install. I can't use the Toolshed for various reasons. Anyway, I downloaded the package using hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes I see two files: 1) datatypes_conf.xml, and 2)

Re: [galaxy-dev] Manually adding new tools from toolshed

2015-01-16 Thread Ryan G
this ToolShed. I guess this is less annoying than maintaining everything on your own. Cheers, Bjoern Am 16.01.2015 um 08:22 schrieb Peter Cock: On Thu, Jan 15, 2015 at 6:57 PM, Ryan G ngsbioinformat...@gmail.com wrote: Because of the way the infrastructure for my Galaxy instance is set

Re: [galaxy-dev] Manually installing rsem_datatypes package from toolshed

2015-01-22 Thread Ryan G
PM, Ryan G ngsbioinformat...@gmail.com wrote: I'm trying to manually install rsem_datatypes package into my local Galaxy install. I can't use the Toolshed for various reasons. Anyway, I downloaded the package using hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes

Re: [galaxy-dev] Problem using FastQC in Galaxy

2015-01-05 Thread Ryan G
I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves. One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single

Re: [galaxy-dev] Mercurial is out of date for Toolshed

2015-01-05 Thread Ryan G
a Trello card to track this issue: https://trello.com/c/9A9uIav0 Let us know if you happen to find a workaround for this issue. -John On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com wrote: I've been trying to track down why I can't get anything from the toolshed

[galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
Hi all - I've got a bunch of fatsq files uploaded into a data library in Galaxy. The underlying files is gzipped however Galaxy strips the .gz from the filename and displays it as .fastq. When the python wrapper rgFastQC.py gets called, it correctly sees the fastq.gz file. The wrapper creates a

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
To (I think) fix this, I changed line 50 in rgFastQC.py from infname = self.opts.inputfilename to infname = self.opts.input This will force FastQC to look at the real file and not the renamed dataset. On Mon, Jan 12, 2015 at 12:20 PM, Ryan G ngsbioinformat...@gmail.com wrote: Yes, I'm doing

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-13 Thread Ryan G
a long term storage perspective this is not ideal - so I am keen for better handling of gzipped files within Galaxy (particularly within libraries which we use for raw data). Peter On Mon, Jan 12, 2015 at 5:20 PM, Ryan G ngsbioinformat...@gmail.com wrote: Yes, I'm doing a link to file

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
file system, so for usegalaxy.org ALL their data files are compressed but Galaxy can ignore this complexity. Peter On Mon, Jan 12, 2015 at 3:15 PM, Ryan G ngsbioinformat...@gmail.com wrote: Hi all - I've got a bunch of fatsq files uploaded into a data library in Galaxy. The underlying

Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

2015-01-12 Thread Ryan G
Galaxy just symlinks to existing files? I thought that was not possible with gzipped files (for the reasons given below). Perhaps this is not being blocked, leading to the confused state you're seeing? Peter On Mon, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformat...@gmail.com wrote: Galaxy

Re: [galaxy-dev] Mercurial is out of date for Toolshed

2015-01-08 Thread Ryan G
at 10:56 AM, Ryan G ngsbioinformat...@gmail.com wrote: Yes, I think I found the root cause...its because the Galaxy egg for mercurial is using an older version of Mercurial that has this known bug. The only real fix is to upgrade the Galaxy egg to mercurial 3.x. The only way I know

Re: [galaxy-dev] Mercurial is out of date for Toolshed

2015-01-08 Thread Ryan G
I just installed it. It worked. It did add a new tool section in the toolbox, but at least the installation problem is solved. I think the new section is a separate issue. I'd consider this a good fix. On Thu, Jan 8, 2015 at 10:36 AM, Ryan G ngsbioinformat...@gmail.com wrote: Yes, I

Re: [galaxy-dev] Mercurial is out of date for Toolshed

2015-01-07 Thread Ryan G
On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com wrote: I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what

[galaxy-dev] SGE integration

2015-01-29 Thread Ryan G
I'm trying to get my instance of Galaxy working with Sun Grid Engine. The page https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster is not 100% clear on how to do this but I here's what my job_conf.xml looks like: ?xml version=1.0? job_conf plugins plugin

[galaxy-dev] Data Libraries

2015-04-23 Thread Ryan G
Hi all - We are trying to use Galaxy as a mechanism for our sequencing lab to create data libraries for data they generate. I noticed in the docs, only Admins are able to create data libraries. Is there a way to change this? I'd like to give specific users in our group this ability without

Re: [galaxy-dev] Data Libraries

2015-04-24 Thread Ryan G
, Apr 23, 2015 at 4:33 PM Ryan G ngsbioinformat...@gmail.com wrote: Hi all - We are trying to use Galaxy as a mechanism for our sequencing lab to create data libraries for data they generate. I noticed in the docs, only Admins are able to create data libraries. Is there a way to change

[galaxy-dev] new tool works correctly but galaxy thinks it failed

2015-04-28 Thread Ryan G
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded. How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info

Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

2015-04-28 Thread Ryan G
correctly. If yours does, you can set exit_code tags and everything should work. On Tue, Apr 28, 2015 at 11:47 AM Ryan G ngsbioinformat...@gmail.com wrote: ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would

Re: [galaxy-dev] optional tool arguments

2015-04-29 Thread Ryan G
29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote: Hi - I'm implementing a new

Re: [galaxy-dev] Data Libraries

2015-04-29 Thread Ryan G
for each project inside a Sequencing library. Would that work? Nicola Il 24.04.2015 13:10 Ryan G ha scritto: This could work. In the long run though, after sequencing for a project, we'd like them people in the sequencing lab to be able to add the data to Galaxy in project specific

Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

2015-04-29 Thread Ryan G
in the future - starting in 15.05 - you will be able to just add detect_errors=exit_code on the command tag to get a more sensible default behavior. https://github.com/galaxyproject/galaxy/pull/117 -John On Tue, Apr 28, 2015 at 12:12 PM, Ryan G ngsbioinformat...@gmail.com wrote: stdio exit_code

Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

2015-04-28 Thread Ryan G
the stdio tag, since due to a historical design choice by default any output on stderr is treated as an error. See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com wrote: Hi - I implemented a tool I us

[galaxy-dev] Can a tool retrieve a user's API KEY?

2015-05-18 Thread Ryan G
I'm trying to create a tool that user's can use that will interact with Galaxy 's API, however the tool needs to be able to determine the user's API key.Is this possible? Can a tool determine what the user's API key is when the user actually runs the tool?

[galaxy-dev] input dataset(s) and collections

2015-06-23 Thread Ryan G
Hi all - I'm constructing a wrapper for a tool I have and the input to the tool can be: 1) a single fastq file (single end sample) 2) multiple singled-end fastq files 3) a single paired-end sample 4) multiple paired-end samples. I have cases #1 and #2 handled, however case #3 is presenting a

[galaxy-dev] Bug in commit 38679a0

2015-06-18 Thread Ryan G
In scripts/functional_tests.py, line 71, the change is causing a directory called test-data,https://github.com/galaxyproject/galaxy- test-data.git to get created. I'm not sure that's the intention of this fix. default_galaxy_test_file_dir is assigned to test_dir, then never used again. test_dir

Re: [galaxy-dev] input dataset(s) and collections

2015-06-25 Thread Ryan G
On Tue, Jun 23, 2015 at 12:58 PM, Ryan G ngsbioinformat...@gmail.com wrote: Hi all - I'm constructing a wrapper for a tool I have and the input to the tool can be: 1) a single fastq file (single end sample) 2) multiple singled-end fastq files 3) a single paired-end sample 4

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

2015-06-25 Thread Ryan G
Hi all - I'm trying to figure out how to script the ability to upload data (fastq) files to Galaxy via the API. I can get the Library's root_folder_id, but am unsure of what the API call is to upload a file. I'm constructing this dictionary: data = {} data['folder_id'] = galaxyFolderId

[galaxy-dev] Custom Tool Dev Questions

2015-06-19 Thread Ryan G
Hi all - I have a tool which is essentially an entire NGS pipeline bundled into a perl script and associated modules. I'd like to offer this tool to users via Galaxy. I'm trying to pass a bunch of fastq files to the tool, but noticed that operating on multiple datasets creates a separate job for

Re: [galaxy-dev] Custom Tool Dev Questions

2015-06-19 Thread Ryan G
before using your tool - but the creator is actually really nice - I think it makes it very easy to build large lists of pairs. Hope this helps - happy to provide more details, -John On Fri, Jun 19, 2015 at 11:24 AM, Ryan G ngsbioinformat...@gmail.com wrote: Hi all - I have a tool which

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

2015-06-26 Thread Ryan G
By browsing the api code, I discovered library_contents.py that looks like it should be used. Why this and not folder_contents.py? There seems to be overlap of these two. I would expect to upload files to folders within libraries... On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat

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

2015-06-26 Thread Ryan G
/galaxy/api/library_contents.py#L144 Hope this helps. M. On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com wrote: By browsing the api code, I discovered library_contents.py that looks like it should be used. Why this and not folder_contents.py? There seems to be overlap

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

2015-06-26 Thread Ryan G
: 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

[galaxy-dev] bowtie dataset pair input

2015-06-24 Thread Ryan G
Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list. Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie

Re: [galaxy-dev] functional tests / database lock

2015-06-16 Thread Ryan G
, 2015 at 11:15 AM, Ryan G ngsbioinformat...@gmail.com wrote: Is there a known cause for this? On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsora...@tiscali.it wrote: Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL. Cheers, Nicola Il 12.06.2015 16:43

Re: [galaxy-dev] functional tests / database lock

2015-06-17 Thread Ryan G
somewhere. What's the point in having the tests if they always fail? On Tue, Jun 16, 2015 at 1:12 PM, Ryan G ngsbioinformat...@gmail.com wrote: I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I

Re: [galaxy-dev] functional tests / database lock

2015-06-17 Thread Ryan G
Thanks. Let me know how I can help. On Wed, Jun 17, 2015 at 12:08 PM, Dannon Baker dannon.ba...@gmail.com wrote: Thanks, I'll take a look. Non-tool-based functional tests should *not* fail out of the box, and we'll fix them :) On Wed, Jun 17, 2015 at 12:04 PM Ryan G ngsbioinformat

[galaxy-dev] functional tests / database lock

2015-06-12 Thread Ryan G
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the

[galaxy-dev] keep job output and scripts on failed tests

2015-06-12 Thread Ryan G
I'd like to recommend a change. If jobs fail to run during functional tests, I'd like to keep the failed job files around to be examined. I added the following to do so: +++ scripts/functional_tests.py @@ -372,6 +372,7 @@ def main():

Re: [galaxy-dev] functional tests / database lock

2015-06-12 Thread Ryan G
Is there a known cause for this? On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsora...@tiscali.it wrote: Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL. Cheers, Nicola Il 12.06.2015 16:43 Ryan G ha scritto: Hi all - I'm running functional tests on a set

[galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure

2015-06-12 Thread Ryan G
The functional test for this tool fails. Looking at the XML wrapper, it looks like $comments is invalidit doesn't exist anywhere else in the xml file. I know that comments can be specified multiple times however there is no way to get the comments fields to appear multiple times in the UI as

Re: [galaxy-dev] keep job output and scripts on failed tests

2015-06-12 Thread Ryan G
GALAXY_TEST_NO_CLEANUP is set, run_tests.sh shouldn't remove the test output. This is great when debugging why a test is failing. Peter On Fri, Jun 12, 2015 at 4:29 PM, Ryan G ngsbioinformat...@gmail.com wrote: I'd like to recommend a change. If jobs fail to run during functional tests, I'd like

Re: [galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure

2015-06-12 Thread Ryan G
done On Fri, Jun 12, 2015 at 11:33 AM, Nicola Soranzo nsora...@tiscali.it wrote: Hi Ryan, please open a pull request at https://github.com/galaxyproject/tools-devteam The file is in tools/picard/ directory. Thanks, Nicola Il 12.06.2015 17:23 Ryan G ha scritto: The functional test

[galaxy-dev] minor visual bug found when using Firefox

2015-06-01 Thread Ryan G
In the workflow editor, if you add an Input dataset collection, the Collection Type: shows list. No dropdown arrow appears using Firefox. A dropdown arrow appears when you mouse over using Chrome. In Firefox, if you mouse over where the dropdown box should be, you can still click to choose list

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

2015-06-29 Thread Ryan G
Perfect. Thanks! On Fri, Jun 26, 2015 at 6:02 PM, Martin Čech mar...@bx.psu.edu wrote: The second link leads to an endpoint that does exactly that. M. On Fri, Jun 26, 2015 at 4:43 PM Ryan G ngsbioinformat...@gmail.com wrote: What if the data is not in the history? Ie we received ngs

[galaxy-dev] Feature Request: Ability to specify a directory to read xml files for tool configuration

2015-06-11 Thread Ryan G
Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of: section id=myTools name=Custom Tools tool file=mytools/tool1.xml / tool

Re: [galaxy-dev] Feature Request: Ability to specify a directory to read xml files for tool configuration

2015-06-11 Thread Ryan G
if it is not and 'polling' which will use # a less efficient monitoring scheme that may work in wider range of scenarios # than the watchdog default. #watch_tools = False Cheers, Bjoern Am 11.06.2015 um 18:09 schrieb Ryan G: Right now for each tool I have, I have to list the xml

[galaxy-dev] Galaxy in Amazon

2015-08-19 Thread Ryan G
Hi all - We are running a local instance of Galaxy on our internal infrastructure. It seems to be going well. We've gotten to the point where we are ready to migrate our NGS data to Amazon for storage in S3. We are also looking at how Galaxy can be used in Amazon. Specifically, we are

Re: [galaxy-dev] galaxy.ini

2015-07-14 Thread Ryan G
It's in your config/ directory. Sent from my iPhone On Jul 14, 2015, at 6:35 AM, Bryan Hepworth bryan.hepwo...@newcastle.ac.uk wrote: Hi For the woefully inept, where in the heck is galaxy.ini stored? I saw the documentation that said change 127.0.0.1 to 0.0.0.0 and the file

[galaxy-dev] Workflow editor stuck on loading workflow

2015-07-14 Thread Ryan G
It looks like a recent commit since 6/26 to 15.05 is break the workflow editor. I have a pipeline I'm trying to edit. I updated my instance of Galaxy and now when I try to edit a workflow, the editor is stuck at Loading workflow editor. ___

Re: [galaxy-dev] Workflow editor stuck on loading workflow

2015-07-14 Thread Ryan G
Hmmm this only happens on a specific workflow. How can I debug this? On Tue, Jul 14, 2015 at 3:37 PM, Ryan G ngsbioinformat...@gmail.com wrote: It looks like a recent commit since 6/26 to 15.05 is break the workflow editor. I have a pipeline I'm trying to edit. I updated my instance

Re: [galaxy-dev] Error sorting or uploading Bam File

2015-07-17 Thread Ryan G
I would think the correct approach would be to allow any bam file and if a tool requires a coordinate sorted bam and one is not provided it would make sense for the tool to fail with an error. Does galaxy itself require a coordinate sorted bam or this this so the majority of tools can

Re: [galaxy-dev] Workflow editor stuck on loading workflow

2015-07-15 Thread Ryan G
of the tools in your workflow. Cheers, Bjoern Am 14.07.2015 um 22:02 schrieb Ryan G: Hmmm this only happens on a specific workflow. How can I debug this? On Tue, Jul 14, 2015 at 3:37 PM, Ryan G ngsbioinformat...@gmail.com wrote: It looks like a recent commit since 6/26 to 15.05 is break

[galaxy-dev] tabular file displayed without tabs

2015-10-26 Thread Ryan G
Hi - I have a tools that generates a tab-delimited text file as output. when I click the eye icon to view the data, all the fields are compressed as if there were no tabs. If I expand the history view, the little preview window shows the contents as tabbed. I've verified that the spaces are

Re: [galaxy-dev] tabular file displayed without tabs

2015-10-28 Thread Ryan G
The file is an output from a tool and in the tool's xml, its format is tabular. On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Ryan, > > is it recognised as 'tabular'? > > Ciao, > Bjoern > > Am 27.10.2015 um 04:42 schrieb R

[galaxy-dev] Cloudman vs StarCluster

2015-11-11 Thread Ryan G
Hi all - Our organization requires us to use a specific AMI (with a specific flavor of linux) that isn't supported by Cloudman. Its taking us a bit of time to get this combination working. Its taken more than 3 weeks and we still don't have Galaxy / Cloudman running. I could probably do the

Re: [galaxy-dev] feature request

2015-11-09 Thread Ryan G
Thanks. On Mon, Nov 9, 2015 at 4:40 PM, Martin Čech <mar...@bx.psu.edu> wrote: > Created it for you here: > https://github.com/galaxyproject/galaxy/issues/1045 > > > On Mon, Nov 9, 2015 at 4:39 PM Ryan G <ngsbioinformat...@gmail.com> wrote: > >> Yes, I'll do

[galaxy-dev] feature request

2015-11-09 Thread Ryan G
I'd put this into Trello, but Trello is blocked from my place of business... I have a data library with over 200 files in it. Half of them are "clipped" and the other half are not. I'd like to be able to search and display a subset of files in the data library. This will make selecting the

Re: [galaxy-dev] feature request

2015-11-09 Thread Ryan G
Yes, I'll do it there. On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Ryan, > > can you create a github issue with this suggestion :) > > Thanks, > Bjoern > > Am 09.11.2015 um 22:37 schrieb Ryan G: > > I'd put this into T

[galaxy-dev] User API keys with External (LDAP) authentication disabled?

2015-10-07 Thread Ryan G
Hi all - I have external authentication established with our enterprise wide LDAP working with Galaxy. I just noticed that I can no longer manage API keys for users from the Admin Page -> API Keys. I get "Access to Galaxy user controls is disabled. User controls are disabled when Galaxy is

Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Ryan G
I just recently submitted a patch that will display all the environment variables being passed to Galaxy in pastor.log. That should help you determine if the variables are set and to what. Please excuse any typos -- Sent from my iPhone > On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD >

Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Ryan G
Here is the pull request: https://github.com/galaxyproject/galaxy/pull/823 You can see what file was edited On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD < floreline.touch...@gmail.com> wrote: > Thank you ! Can you tell me which files are to update or download ? > I installed my

Re: [galaxy-dev] User API keys with External (LDAP) authentication disabled?

2015-10-08 Thread Ryan G
n interface right now. I noted this bug just the other >> day and intended to fix it as it applied to us as well. >> Until then, you can easily change the API key manually in the database. >> >> Cheers, >> Eric >> >> 2015-10-07 16:20 GMT-05:00 Ryan G <ngsbi

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Ryan G
Hi all - In regards to external user authentication that I have working now (see thread below). When users try to go to the actual Galaxy page, they get the message: On Thu, Oct 1, 2015 at 4:10 PM, Ryan G <ngsbioinformat...@gmail.com> wrote: > I finally got around to this and all i

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Ryan G
. Is there a way to do this? I didn't see anything obvious and was thinking of adding a parameter to galaxy.ini and have Galaxy automatically forward them after 5 seconds or so. Ryan On Tue, Oct 13, 2015 at 10:49 AM, Ryan G <ngsbioinformat...@gmail.com> wrote: > Hi all - In regards to

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Ryan G
://mycompay.com/galaxy which is where they will be authenticated. Users never see http://galaxy.mycompany.com:8080they will always see http://mycompay.com/galaxy On Tue, Oct 13, 2015 at 12:36 PM, Eric Rasche <e...@tamu.edu> wrote: > > > On 10/13/2015 11:34 AM, Ryan G wrote: > >

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Ryan G
at 11:10 AM, Eric Rasche <e...@tamu.edu> wrote: > Hi Ryan, > > On 10/13/2015 09:50 AM, Ryan G wrote: > > Hi all - In regards to external user authentication that I have working > > now (see thread below). When users try to go to the actual Galaxy pag

[galaxy-dev] External User Authenticaion

2015-08-31 Thread Ryan G
Hi all - I'm trying to use external user authentication with Galaxy. The external authentication passes to Galaxy the username with the mail domain at HTTP_USER. In galaxy.ini, I enable: use_remote_user = True When I try to access Galaxy, I get the message: Galaxy is configured to authenticate

Re: [galaxy-dev] External User Authenticaion

2015-09-03 Thread Ryan G
SER there). Let me know if this doesn't sort it out for you and we > can dig deeper! > > -Dannon > > On Mon, Aug 31, 2015 at 3:42 PM, Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> Hi all - I'm trying to use external user authentication with Galaxy. The >> external au

Re: [galaxy-dev] External User Authenticaion

2015-09-08 Thread Ryan G
/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49 > > -Dannon > > On Thu, Sep 3, 2015 at 1:51 PM, Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> It turns out our authentication system passes a header 'HTTP_MAIL' which >

Re: [galaxy-dev] External User Authenticaion

2015-10-01 Thread Ryan G
_href parameter to a different website, but they still get the "Access to Galaxy user controls is disabled". I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I think at that point its too late. On Tue, Sep 8, 2015 at 4:05 PM, Ryan G <ngsbioinformat...@gmail.com> wrote: > Y

[galaxy-dev] External Pipeline Cleanup

2015-10-05 Thread Ryan G
Hi all - For various reasons, we've had to implement our pipelines external to Galaxy, but still give Galaxy the ability to run them. I've accomplished this by having the Galaxy tool wrapper call the external app to launch the pipelines. My problem is that when a user aborts the tool, the tool

Re: [galaxy-dev] tabular file displayed without tabs

2016-06-14 Thread Ryan G
same sort of error? > * Do you see any javascript errors in the console when attempting the > viewing? (how to here: http://webmasters.stackexchange.com/a/77337) > > On Fri, May 27, 2016 at 12:42 PM, Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> The format is list

Re: [galaxy-dev] tabular file displayed without tabs

2016-05-27 Thread Ryan G
gt; side of the 'Analyze Data' page), what does it list the 'Format' as? > 'tabular'? (This is also listed as 'Format' in the expanded view itself). > > On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> Odd because I have another tabu

[galaxy-dev] Bug Found: 2 tabs in browser open to different histories confuses tools

2016-05-31 Thread Ryan G
Hi all - I think I found a bug. I have two histories open in two separate tabs in Chrome. When I try to run a tool and select an item from my history, the wrong history items are displayed. Ryan ___ Please keep all replies on the list by

Re: [galaxy-dev] Login reguried causing nested main page loading

2016-01-11 Thread Ryan G
I've seen this as well. I find that restarting galaxy fixes the problem but I'd love to know the underlying cause. Please excuse any typos -- Sent from my iPhone > On Jan 11, 2016, at 5:08 AM, Christian Brenninkmeijer > wrote: > > Hi All, > > I

[galaxy-dev] Restricting tool input to 1 dataset instead of multiple

2016-02-24 Thread Ryan G
Hi all - I'm creating a tool in Galaxy that takes as input several datasets for different variables. For each variable, I want to restrict the input to a single dataset. The docs, https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax, indicate type="data" needs to be set for a dataset from

[galaxy-dev] Custom tool with multiple inputs for different datasets. How to preferrentially select

2016-02-24 Thread Ryan G
Next question - My custom tool take as input mulitple datasets from different tools and collates all the information. For instance, 1 input as tabular input, sampleManifest, another input is also tabular, expressionData. When the tool is display, both entries default to the most recent tabular

[galaxy-dev] Cloudman & AWS IAM_PROFILE support?

2016-03-14 Thread Ryan G
Hi - Does Cloudman support IAM_PROFILES? We run our instances within a VPC and assign an IAM_PROFILE to the ec2 instances so that they have access to resouces. Does Cloudman have this support? ___ Please keep all replies on the list by

Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

2016-03-15 Thread Ryan G
We actually have galaxy running within a VPC now. The problem we're running into is that when ec2 instances get created they don't have an I_am profile attached to them so they can't get access to S3 resources. This should just be a parameter past to AWS when the instances get created to attach

Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

2016-03-21 Thread Ryan G
We Iocally compile 2.7.8 and keep it in a distinct location that our paths references. This is very easy and has worked well for us. Please excuse any typos -- Sent from my iPhone > On Mar 21, 2016, at 5:32 PM, Peter Cock wrote: > > Hi D. K., > > We're currently

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

2016-03-03 Thread Ryan G
, Nate Coraor <n...@bx.psu.edu> wrote: > On Tue, Mar 1, 2016 at 1:19 PM, Ryan G <ngsbioinformat...@gmail.com> > 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 &

[galaxy-dev] Galaxy 15.10 Jobs not running

2016-03-01 Thread Ryan G
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 been made to revert something, but I'm not clear what. Is there something going on

Re: [galaxy-dev] tabular file displayed without tabs

2016-05-23 Thread Ryan G
narrowing the window and getting more space as you expand the > window) would reflect that. > > Carl > > On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> The file is an output from a tool and in the tool's xml, its format is >>

[galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

2016-07-27 Thread Ryan G
Hi all - We are using a SSO system so that user's authenticate externally from Galaxy. when I impersonate a user then try to log out as that user, I'm unable to. I get the page " Access to Galaxy user controls is disabled User controls are disabled when Galaxy is configured for external

Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

2016-07-27 Thread Ryan G
eck it > out today. > > On Wed, Jul 27, 2016 at 12:44 PM Ryan G <ngsbioinformat...@gmail.com> > wrote: > >> Hi all - We are using a SSO system so that user's authenticate externally >> from Galaxy. >> >> when I impersonate a user then try to log out as

[galaxy-dev] Removing job in error state

2016-08-03 Thread Ryan G
Hi - In the Manage Jobs admin job, I have a job from a user that never ran successfully. It shows: Job ID User Last Update Tool State Inputs Command Line Job Runner PID/Cluster ID 12772 u...@company.com 654 hours ago cshl_fastx_collapser new 13653 error None None None How do I remove this job?

Re: [galaxy-dev] Removing job in error state

2016-08-04 Thread Ryan G
the very last option. > > > Hans-Rudolf > > > On 08/04/2016 06:02 AM, Ryan G wrote: > >> Hi - In the Manage Jobs admin job, I have a job from a user that never >> ran successfully. It shows: >> Job ID UserLast Update ToolState Inputs C

[galaxy-dev] showing progress on running tasks

2016-07-08 Thread Ryan G
Hi all - I know this isn't currently a feature, but wanted to find out about what it would take to implement We developed some custom tools that are long runningmultiple hours. The tools run through various steps of an analysis. Is there a way to display progress of a task in the

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

2016-07-08 Thread Ryan G
his problem. > > Thanks, > > Martin > >> On Fri, Jul 8, 2016 at 10:34 AM Ryan G <ngsbioinformat...@gmail.com> wrote: >> Hi all - I know this isn't currently a feature, but wanted to find out about >> what it would take to implement >> >> We d

Re: [galaxy-dev] provide a field to upload a file as part of tool input

2016-08-05 Thread Ryan G
I figured out the optional part (RTFM to myself) On Fri, Aug 5, 2016 at 6:54 PM, Ryan G <ngsbioinformat...@gmail.com> wrote: > Hi all - I have a custom tool that can optionally take a file as input. > > Right now, users have to upload the file into their history, then select

[galaxy-dev] provide a field to upload a file as part of tool input

2016-08-05 Thread Ryan G
Hi all - I have a custom tool that can optionally take a file as input. Right now, users have to upload the file into their history, then select the file when running the tool. Is there a way to let the user select a file local on their computer as input to the tool, then when run, the file is

Re: [galaxy-dev] Development/production instances updates management

2016-09-02 Thread Ryan G
We do exactly this. We have a staging instance, and a production instance. Both exist in a single git repo as separate branches. The main different for this is that the staging and production config file point to different port and database instances. We also maintain a staging and production

[galaxy-dev] Converting an internal user to an external user

2016-09-07 Thread Ryan G
Hi all - I'm having a problem with a user account and Galaxy getting confused with it being internal vs external. When we first set up galaxy, we were using Galaxy's internal authentication system. This worked well but all our users then had another password to keep track of. We activated

Re: [galaxy-dev] Converting an internal user to an external user

2016-09-07 Thread Ryan G
ne coming > from your external authentication system. > > However, be very careful, whenever you manually interact with the Galaxy > PostgreSQL database. Make sure you have an up-to-date back-up. > > Hope this helps, > Hans-Rudolf > > > > > On 09/07/2016 05:27 PM, Ry

Re: [galaxy-dev] Converting an internal user to an external user

2016-09-07 Thread Ryan G
Ok I got it. I had to update the email address field to match what the REMOTE_USER variable was being set my Apache. On Wed, Sep 7, 2016 at 1:41 PM, Ryan G <ngsbioinformat...@gmail.com> wrote: > Sorry, missed your other questions... > > external authentication via apache...ye

[galaxy-dev] Elastic Bean Stalk

2016-11-15 Thread Ryan G
Hi all - I was wondering, if we deploy Galaxy in AWS, can we take advantage of Elastic BeanStalk to scale our instances based on demand instead of trying to configure Galaxy to perform well for our users? Ryan ___ Please keep all replies on