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

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

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

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

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

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

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Re: [galaxy-dev] Mercurial is out of date for Toolshed

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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?

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

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

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

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

Re: [galaxy-dev] Custom Tool Dev Questions

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

/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

: 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

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 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

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

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():

[galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure

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

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

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

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

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] Galaxy in Amazon

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

[galaxy-dev] Workflow editor stuck on loading workflow

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] Error sorting or uploading Bam File

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

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

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

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

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

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

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

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?

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

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

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] External User Authenticaion

://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

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

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

/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

_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

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

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

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

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

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

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?

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?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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