The wiki is unclear on how the user-data should be formatted when
configuring the AMI.
>From here <http://bitbucket.org/galaxy/galaxy-central/wiki/cloud>
"The user data must follow the following format:
cluster_name: <DESIRED CLUSTER NAME>
password: <DESIRED Galaxy CloudMan WEB UI PASSWORD>
access_key: <YOUR AWS ACCESS KEY>
secret_key: <YOUR AWS SECRET KEY>"
and then here<http://bitbucket.org/galaxy/galaxy-central/wiki/Cloud/GettingStarted>
"User data must follow the following format
'<CLUSTER_NAME>|<AWS_ACCESS_KEY>|<AWS_SECRET_KEY>|<Desired Galaxy Cloud
It's the top format that is correct, isn't it?
Curtin University, Western Australia
Hi Galaxy Team,
do you have any prevision of incorporating this new Illumina short reads
Res.');> 2010 Oct 27 Stampy: A statistical algorithm for sensitive and fast
mapping of Illumina sequence reads.) in Galaxy?
Has any galaxy user tried this new program?
Laboratory of Gene Expression in Eukaryotes
Departamento de Bioquímica
Instituto de Química
Universidade de São Paulo
Av. Prof. Lineu Prestes 748 sala 1200
05508-000 São Paulo, SP
Does anyone have problem with CAPRET Com&Uni function recently? I submit the jobs, but the status is always "running"? The website problem? Thanks.
Haiyan Lei, Ph.D.
Bld 5, Rm b1-04
Bethesda MD 20892
Polymorphic variations were retrieved from a sequenced data (aligned to hg18). The output file contains the chr and the position but no (rs number). The tab delimited file with map extension is
Chr pos # pos
1 82496 0 82496
1 91549 0 91549
1 98173 0 98173
1 696970 0 696970
Could you please let me know if there is way with galaxy to retrieve the rs number for these SNPs? I am open to any solution!
Many thanks for your help,
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The out.data is simply picked up by galaxy:
As long as you define your variable capturing the output and also in
your tool.xml file.
Make sure the output is defined as "data" in the tool.xml file.
Initially I thought the same thing, but the piping is not needed with
'>', worse, it doesn't work like that.
Gerrit, Renaud and others,
We apologize for the inconvenience - it seems that you have uncovered a bug that has been corrected in our development repo, but has not yet made it to our distribution repo. This fix should reach the distribution repo some time next week. Thanks very much for reporting this!
On Nov 11, 2010, at 9:34 AM, gerrit wrote:
> Hi Greg,
> I did a test and got galaxy as you said:
> hg clone http://bitbucket.org/galaxy/galaxy-dist
> Installed and same error message was given.
> Then I tried the galaxy-central clone:
> hg clone http://bitbucket.org/galaxy/galaxy-central
> Installed and now the datasets from the history can be loaded into the data library!
> I've also installed the galaxy-dist on a few pcs at our lab and the same error remains! I do not want to switch to the galaxy-central fork because of the active development that can introduce bugs. There is quite a few researchers using our galaxy server so we need a stable version.
> The galaxy that you're running on http://main.g2.bx.psu.edu/ is a copy of the galaxy-dist, if I'm correct. I would like to reproduce the error, but cannot import any history datasets into a data library folder (do not have permissions). For a test is it possible that you can create a temporary data library for me. You can remove it as soon as I'm done. My user account is gerrit.botha(a)gmail.com.
> Thanks for the help,
> On Wed, Nov 10, 2010 at 4:46 PM, gerrit <gerrit.botha(a)gmail.com> wrote:
> Hi Greg,
> It is a long time since I've read the documentation on your site, but since I've started with galaxy I checked it out like this:
> hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
> The strange thing is then when I run "hg heads" it shows the exact version which you have.
> changeset: 4354:d681ef7538ed
> tag: tip
> user: Greg Von Kuster <greg(a)bx.psu.edu>
> date: Wed Sep 29 12:39:39 2010 -0400
> summary: Fix for rendering hidden widget field values associated with library templates whose fields are displayed on the upload form when importing a dataset from the current history. Added new functional test to cover behavior.
> I will test a checkout with the other update site.
> On Wed, Nov 10, 2010 at 4:22 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
> I am not able to reproduce this problem, and in fact, the message being displayed looks like it comes from very old code ( this particular message "Invalid item id..." is no longer in the most recent version of the code. From where are you getting your updates? You should be getting them from here:
> hg clone https://<your account>@bitbucket.org/galaxy/galaxy-dist
> To make sure you are running the latest distribution, go to your Galaxy root directory and type:
> hg heads
> and you should see
> 4354 d681ef7538ed
> On Nov 10, 2010, at 8:08 AM, gerrit wrote:
>> Dear Galaxy Users,
>> Since I've updated my Galaxy version I'm unable to import any dataset from my history into my data library. It returns a message of e.g. "Invalid item id (1464) specified".
>> I then did a complete new test installation to make sure that this problem wasn't because of the update. But the error still remains. I've included a screen shot in which the error is reported.
>> When I queried the database the dataset id does exist in the history_dataset_association table.
>> I went through the paster.log file and found the following warning message: Unknown library item type: <class 'galaxy.model.
>> HistoryDatasetAssociation'>. Can it be that this class is not loaded or found?
>> Is anyone experiencing the same problem?
>> galaxy-user mailing list
> Greg Von Kuster
> Galaxy Development Team
Greg Von Kuster
Galaxy Development Team
I also get the same error.
1. install a fresh Galaxy from the repository (via: hg clone
2. run the setup.sh script
3. create a user 'test'
4. stop galaxy, make user 'test' admin in universe_wsgi.ini, restart galaxy
5. create a new data library 'Lib'
6. give the user all permission on this data library
7. upload some fasta file 'seq.fas' via: Get Data > Upload File
8. go to Shared Data > Data Libraries > 'Lib' - Add datasets
9. use upload option: import datasets from current history
10. select file 'seq.fas', and hit 'import to library'
=> Invalid item id (2) specified.
The direct import 'Upload files' in 'Upload files to a data library'
view works fine.
Any help or bug fix is welcome.
UNIVERSITY OF CAPE TOWN
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Dear galaxy users,
My team is involved in the NGS field. We have our own local cluster and we
are looking for a workflow management system. Currently we are trying to set
up and test galaxy.
For our quality control analysis pipeline, R statistical software will be
used. So we want to be able to call R scripts from galaxy.
I know that it is possible and the xy_plot.xml is a really good example
(conditional & when, repeat tags). Also, in this example a <configfile> tag
is used. Within this tag you put your R code. And moreover you can add lines
beginning with only one '#' which will be interpreted with *cheetah template
engine*. This is helpful to create dynamic content of your R code with
respect to your submitted parameters. (an old screencast introduces this
My question is : is there a way to avoid the <configfile> section and to let
all the R code be outside the tool's xml config file? If yes, how can we
specify an output file in the xml conf that will catch, for instance, a
write.table() call in the R script ?
Dear Galaxy Users,
Since I've updated my Galaxy version I'm unable to import any dataset from
my history into my data library. It returns a message of e.g. "Invalid item
id (1464) specified".
I then did a complete new test installation to make sure that this problem
wasn't because of the update. But the error still remains. I've included a
screen shot in which the error is reported.
When I queried the database the dataset id does exist in the
I went through the paster.log file and found the following warning message:
Unknown library item type: <class 'galaxy.model.
HistoryDatasetAssociation'>. Can it be that this class is not loaded or
Is anyone experiencing the same problem?
You can avoid working with wrappers to run 3 scripts (your R-script, a
perl or shell wrapper and the necessary xml file)
to make 1 actually run what you want to do.
I've struggled with this in the previous digests, which are not so
accessible to search-find.
simply put in your tool.xml file:
R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/<your
Rscript.R> --args $inputFile $<any nr of input args> $outputFile
This way you can run any R script in galaxy.
Unfortunately, (also in one of the previous digests), "warnings" in R
are causing an error status, so that once in a while
you will need to add to the end of the cmd line in the above: 2>&-
to ignore these warnings (but also any error message)
My advice is to build and test in shell and galaxy without it and later
add it to get to your output file(s).
So far this has worked for me.
Freddy de Bree
> Date: Tue, 9 Nov 2010 15:20:52 +0100
> From: Anthony Ferrari<ferraria(a)gmail.com>
> To: galaxy-user(a)lists.bx.psu.edu
> Subject: [galaxy-user] plugging R into galaxy
> Content-Type: text/plain; charset="iso-8859-1"
> Dear galaxy users,
> My team is involved in the NGS field. We have our own local cluster and we
> are looking for a workflow management system. Currently we are trying to set
> up and test galaxy.
> For our quality control analysis pipeline, R statistical software will be
> used. So we want to be able to call R scripts from galaxy.
> I know that it is possible and the xy_plot.xml is a really good example
> (conditional& when, repeat tags). Also, in this example a<configfile> tag
> is used. Within this tag you put your R code. And moreover you can add lines
> beginning with only one '#' which will be interpreted with *cheetah template
> engine*. This is helpful to create dynamic content of your R code with
> respect to your submitted parameters. (an old screencast introduces this
> My question is : is there a way to avoid the<configfile> section and to let
> all the R code be outside the tool's xml config file? If yes, how can we
> specify an output file in the xml conf that will catch, for instance, a
> write.table() call in the R script ?
> Best regards,