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
___
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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 wrote:
> Sorry, missed your other questions...
>
> external authentication via apache...yes. Its working well for us.
> The u
s the one 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
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 extern
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
I figured out the optional part (RTFM to myself)
On Fri, Aug 5, 2016 at 6:54 PM, Ryan G 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
> the file when running the tool.
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 up
ot;error" in the 'job' table, eg:
>
> update job set state='error' where id=12772;
>
>
> As always, be very careful when you directly access the PostgreSQL
> database! Make sure your database is properly backed up. And you should
> only consider this
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? I
mation. What revision of Galaxy are you
> running? Are you serving Galaxy at a subdomain or is any other nonstandard
> routing in place? As an admin user, if you just directly navigate
> to http:///user/logout, you get the same
> path-blocked error message?
>
> On Wed, Jul 27, 2016
> On Wed, Jul 27, 2016 at 12:44 PM Ryan G
> 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 that user, I'm unable
>> to. I get the page &
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
authentic
Thanks,
>
> Martin
>
>> On Fri, Jul 8, 2016 at 10:34 AM Ryan G wrote:
>> 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 running.
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 history?
folks would want though I opted not
> to do so originally to avoid configuration bloat for what seemed like a
> very niche case.
>
> On Tue, Jun 14, 2016 at 10:23 AM Ryan G
> wrote:
>
>> No, it happens to all output from this particular tool.
>>
>> I do see a jav
t; * 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
> wrote:
>
>> The format is listed as tabular when I view details.
>>
>> In
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
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right hand
> 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
> wrote:
>
>> Odd because I
re space as you expand the
> window) would reflect that.
>
> Carl
>
> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G
> wrote:
>
>> The file is an output from a tool and in the tool's xml, its format is
>> tabular.
>>
>>
>>
>> On Tue, Oc
o those
> outputs, i.e:
>
> ```
>
>
>
>
>
>
>
>
>
>
> ```
>
> I understand that you would also like to keep the $sraid id in the history,
> right?
> For that you should be able use `label="${sraid}.txt` on your outputs.
>
> Cheers,
> Marius
&
I'm playing around with creating a Galaxy wrapper for custom tool I've
created. My tool takes a single parameter, and SRA ID. In command block,
I have something like this:
${GALAXY_ROOT_DIR}/tools/mycustomtools/doSomething.pl --sra $sraid
Galaxy doesn't like thr $sraid in the
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 trying a locally compiled P
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
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?
___
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00 PM, Nate Coraor wrote:
> On Tue, Mar 1, 2016 at 1:19 PM, Ryan G
> 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
>> obvious problem in the log file.
>>
>
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 wit
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
da
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
This is why I think Galaxy unit tests really need to be up to date and
working thoroughly. Something like this could have been easily caught.
On Thu, Feb 18, 2016 at 7:31 PM, wrote:
> Good evening,
> Having wasted multiple hours it would be helpful to see in the
> documentation that only LOWERC
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 tried to turn on login required in config.in
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 sam
Thanks.
On Mon, Nov 9, 2015 at 4:40 PM, Martin Čech wrote:
> Created it for you here:
> https://github.com/galaxyproject/galaxy/issues/1045
>
>
> On Mon, Nov 9, 2015 at 4:39 PM Ryan G wrote:
>
>> Yes, I'll do it there.
>>
>> On Mon, Nov 9, 2015 at 4:
Yes, I'll do it there.
On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning
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 Trello, but Trell
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 file
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
wrote:
> Hi Ryan,
>
> is it recognised as 'tabular'?
>
> Ciao,
> Bjoern
>
> Am 27.10.2015 um 04:42 schrieb 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
indee
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 applicati
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
> wr
Thanks. I'll try that.
On Tue, Oct 13, 2015 at 12:52 PM, Eric Rasche wrote:
> Howdy Ryan,
>
> On 10/13/2015 11:44 AM, Ryan G wrote:
> > Sorry, maybe I'm not being clear.
> >
> > Galaxy is listening on http://galaxy.mycompany.com:8080
> >
> > U
http://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 wrote:
>
>
> On 10/13/2015 11:34 AM, Ryan G wrote:
> > We have Apache se
11:10 AM, Eric Rasche 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 page,
> > they get the message:
> >
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 wrote:
> I finally got around to this and all is working well. I submitted 2
> p
login
page. 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
wrote:
> Hi all - In regards to external user aut
t 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 > <ma
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 confi
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 ne
_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 wrote:
> Yes, I have a test server I&#
s://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49
>
> -Dannon
>
> On Thu, Sep 3, 2015 at 1:51 PM, Ryan G
> wrote:
>
>> It turns out our authentication system passes a header 'HTTP_MAIL' which
>> contains the us
doesn't sort it out for you and we
> can dig deeper!
>
> -Dannon
>
> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G
> wrote:
>
>> Hi all - I'm trying to use external user authentication with Galaxy. The
>> external authentication passes to Galaxy the usern
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
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 intereste
on workflows
> and the workflow editor and if I encounter this bug and find a fix I
> will let you know,
> -John
>
> On Wed, Jul 15, 2015 at 4:18 PM, Ryan G
> wrote:
> > The error I see is "TypeError: c.effectiveMapOver is not a function" in
> > static/scripts/
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 functi
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
> wrote:
> >
> >> It looks like a rec
Hmmm this only happens on a specific workflow. How can I debug this?
On Tue, Jul 14, 2015 at 3:37 PM, Ryan G 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 of
> Galaxy and
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".
__
It's in your config/ directory.
Sent from my iPhone
> On Jul 14, 2015, at 6:35 AM, Bryan Hepworth
> 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
> name, can't find it to do
Perfect. Thanks!
On Fri, Jun 26, 2015 at 6:02 PM, Martin Čech wrote:
> The second link leads to an endpoint that does exactly that.
> M.
>
>
> On Fri, Jun 26, 2015 at 4:43 PM Ryan G
> wrote:
>
>> What if the data is not in the history? Ie we received ngs data fro
y 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 wrote:
>> What is HDA?
>>
>> Sent from my iPhone
>>
>>> On Jun 2
ct/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
>
> Hope this helps.
>
> M.
>
>> On Fri, Jun 26, 2015 at 12:56 PM Ryan G wrote:
>> By browsing the api code, I discovered library_contents.py that looks like
>> it should be used. Why thi
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 wrote:
> Hi
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
tps://trello.com/c/qCtBBB8n
>
> -John
>
>
> On Tue, Jun 23, 2015 at 12:58 PM, Ryan G
> 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)
> &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 a
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
ol consumes pairs of datasets - you will want to expose an
> option where you are using a parameter like:
>
> collection_type="list:paired" format="fastq" />
>
> and then your users will have to use the data collection creator to
> pair off the datase
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
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_di
Thanks. Let me know how I can help.
On Wed, Jun 17, 2015 at 12:08 PM, Dannon Baker
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
a problem
somewhere. What's the point in having the tests if they always fail?
On Tue, Jun 16, 2015 at 1:12 PM, Ryan G 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
>
we recommend using postgres in production for a reason -
> these sqlite errors are pretty common.
>
> -John
>
>
> On Fri, Jun 12, 2015 at 11:15 AM, Ryan G
> wrote:
> > Is there a known cause for this?
> >
> > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo
> &
done
On Fri, Jun 12, 2015 at 11:33 AM, Nicola Soranzo
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:
>
_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
> wrote:
> > I'd like to recommend a change. If jobs fail to run during functiona
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():
user_library_import_dir=user_library_i
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
Is there a known cause for this?
On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo
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 fu
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
defa
f the watchdog library is available
> > # but won't fail to load Galaxy 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 = Fal
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:
I can do:
I'd add this to Trello but unfortunately my company blocks t
Hi - Are the functional tests for Galaxy supposed to run out of the box?
I'm getting lots a failures with a fresh install in a virtual python
environment.
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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 "li
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?
_
o 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 wrote:
>>
>>
>>
>>
>>
>
folder 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
; On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz 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
>>
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2
fastq files as input. If 1 file is specified, then 1 output file is
created. If 2 inputs are specified, then 2 output files will be created.
How do I specify the optional output parameter?
I'm using this as my tool descrip
rk.
>
> On Tue, Apr 28, 2015 at 11:47 AM Ryan G
> 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 be
>> sufficient to know the tool ran correctly.
>>
>>
&
o 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
> wrote:
> > Hi - I implemented a tool I us into Galaxy but
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
;
> Martin
>
> On Thu, Apr 23, 2015 at 4:33 PM Ryan G
> 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 l
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
givin
ain. 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
> wrote:
> > I tried setting up Galaxy to use
t; -> "EBI SRA" tool, which
> 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 04:4
Do any tools exist to download GEO datasets from NCBI?
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I tried setting up Galaxy to use Sun Grid Engine, but failed miserably. I
removed my config/job_conf.xml hoping Galaxy would revert to its default
state, but jobs are no longer being dispatched. I don't see any errors in
the log.
How can I get Galaxy to 1) use SGE, or 2) revert to its default st
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:
-John
>
>
> On Wed, Jan 21, 2015 at 2:16 PM, Ryan G
> 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
&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) rsem.py
m 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
> wrote:
> >> Because of the way the infrastructure for my Ga
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 py
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