Re: [galaxy-user] Seeing time taken for jobs

2011-01-07 Thread Dannon Baker
Not currently, but this is something we want to implement in the near future, along with a progress indicator for running jobs. -Dannon On Jan 6, 2011, at 6:31 AM, Peter pe...@maubp.freeserve.co.uk wrote: Hi all, I'm curious if there is any way to see how long a task took to complete (or

Re: [galaxy-user] Order of input files when creating a workflow.

2011-01-18 Thread Dannon Baker
Thanks Victor. This is fixed in changeset 4870:65dc28ab157b. This is not on the main galaxy server yet, but when we update you'll see workflow steps preserve an order based on the distance from the top left corner of the workflow editor upon saving. This change will not affect previously

Re: [galaxy-user] fastq and index file upload problems

2011-01-28 Thread Dannon Baker
On Jan 28, 2011, at 2:38 AM, Steve Taylor wrote: You'll need to groom the files to convert them from fastq format to fastqsanger format, which is the format accepted by Galaxy's NGS tools. See the FastqGroomer tool for details. (If you're confident your fastq quality scores are in Sanger

Re: [galaxy-user] Usability - show vs peep, editing attributes, and histories

2011-02-04 Thread Dannon Baker
Thanks for all the feedback! We've not yet discussed it all as a group, but I'd like to offer a quick solution for easily renaming histories. In the history panel, just above the first dataset listed, you should see the name of your current history in lighter text, which if you click on it,

Re: [galaxy-user] Galaxy on Cloud not recognizing .txt files as fastq

2011-03-14 Thread Dannon Baker
Karl, For the URL you're pasting, is it the full path to a file in your s3 bucket, including the protocol (http://) ? For galaxy to recognize that it needs to pull from a URL rather than the contents of the box, you need to use the full string. -Dannon On Mar 14, 2011, at 4:40 PM,

Re: [galaxy-user] postgreSQL 9.0.3 / JSONDecodeError error

2011-03-22 Thread Dannon Baker
Vincent, This issue should be resolved after changeset 5074:89190bcd1ccf, available in the galaxy-central repository. This change will also be available in the near future in the galaxy-dist repository. Thanks! Dannon On Mar 22, 2011, at 12:59 PM, Vincent Le Texier wrote: Hello

Re: [galaxy-user] postgreSQL 9.0.3 / JSONDecodeError error

2011-03-24 Thread Dannon Baker
will be resolved ? Can I apply a patch now and how ? I am facing problem with galaxy-reports and mysql (date_trunc of Postgresql), so it would be better for me to use postgreSQL 9. Vincent Le 3/22/11 6:13 PM, Dannon Baker a écrit : Vincent, This issue should be resolved after changeset 5074

Re: [galaxy-user] is galaxy down?

2011-03-25 Thread Dannon Baker
Keith, We're currently experiencing a small issue with the main galaxy server. If you could wait a while and then retry, it should be fully functional again soon. -Dannon On Mar 25, 2011, at 11:01 AM, Keith E. Giles wrote: I keep getting a SERVER ERROR message. Is galaxy down, or is this

Re: [galaxy-user] Workflows with run time parameters broken?

2011-04-20 Thread Dannon Baker
The issue you're seeing is actually related to improper initialization of the workflow parameters index in the special case where a particular parameter is only used in a rename action and not in a tool step. This is fixed in revision 5400:6cacf178a129. -Dannon On Apr 20, 2011, at 10:28 AM,

Re: [galaxy-user] Workflows with run time parameters broken?

2011-04-20 Thread Dannon Baker
and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 20 Apr 2011, at 15:47, Dannon Baker wrote: The issue you're seeing is actually related

Re: [galaxy-user] Workflows with run time parameters broken?

2011-04-21 Thread Dannon Baker
Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 20 Apr 2011, at 17:44, Dannon Baker wrote: I'll take a look

Re: [galaxy-user] Move data between histories?

2011-04-28 Thread Dannon Baker
Yes, you can copy datasets to other histories, no need to re-upload. To do this, click on Options in the history panel, and then Copy Datasets. From here, you can pick a source history (defaulted to the current active history), select the datasets to be copied, and then choose a destination

Re: [galaxy-user] How to load/import saved workflow .ga files into Galaxy?

2011-05-17 Thread Dannon Baker
On the workflows landing page you should find an option to Upload or import workflow in the top right. Clicking that will allow you to supply a URL to a shared galaxy workflow, or in your case paste in the contents of the .ga file in the Encoded workflow box and it should work. Direct file

Re: [galaxy-user] can I merge histories?

2011-06-14 Thread Dannon Baker
Yes, you can copy datasets from one history to another. In the history panel, click Options, and then Copy Datasets to do so. -Dannon On Jun 14, 2011, at 12:36 PM, Robert Curtis Hendrickson wrote: Folks, Is there some way I can merge histories? I ran a workflow on 3 different samples

Re: [galaxy-user] Workflow API

2011-07-12 Thread Dannon Baker
My question is how I can modify the script to accept multiple inputs (i.e. how do I define which files in the input folder I want to be each input) and if there's a way to specify runtime parameters. For instance, the workflow I want to execute has a filter step on a tabular input item as

Re: [galaxy-user] renaming dataset in workflow

2011-07-29 Thread Dannon Baker
While this is not currently possible, we have recently discussed exposing extra fields for use in both parameters and rename actions. If you're interested, I've created a bitbucket enhancement request

Re: [galaxy-user] line estimation for pileup generation

2011-08-25 Thread Dannon Baker
=== Please use Reply All when responding to this email! === As a first step, please confirm an exact line count for the files. See the Line/Word/Character count tool in the Text Manipulation section to do this. If the estimate is significantly off, please share the history with me and I'll

Re: [galaxy-user] line estimation for pileup generation

2011-08-25 Thread Dannon Baker
again. Austin On Thu, Aug 25, 2011 at 3:19 PM, Dannon Baker dannonba...@me.com mailto:dannonba...@me.com wrote: As a first step, please confirm an exact line count for the files. See the Line/Word/Character count tool in the Text Manipulation section to do this. If the estimate

Re: [galaxy-user] Adding new tools in Galaxy

2011-10-06 Thread Dannon Baker
Makais, Any type of command line tool, whether script or a binary executable, can be used by Galaxy as long as it's properly installed on the system and accessible to the Galaxy user. See http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set for more details on

Re: [galaxy-user] Adding new tools in Galaxy

2011-10-06 Thread Dannon Baker
Makais, Any type of command line tool, whether script or a binary executable, can be used by Galaxy as long as it's properly installed on the system and accessible to the Galaxy user. See http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set for more details on

Re: [galaxy-user] Zoom function on workflow editor?

2011-10-20 Thread Dannon Baker
Arthur, There is no zoom for the main editor window, though you can use(and resize) the little mini view in the bottom right corner to move around the workflow quickly. You could also use the browser-level zoom (in Chrome and Firefox, at least) to see much more at a time. -Dannon On Oct

Re: [galaxy-user] Issue about uploading data

2011-10-20 Thread Dannon Baker
Nandan, Have you tried using our FTP upload process? This is much more robust than the standard upload, especially for large files. See http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP -Dannon On Oct 20, 2011, at 7:05 PM, Nandan Deshpande wrote: Hi, My user id is

Re: [galaxy-user] Map with Bowtie for Illumina (version 1.1.2)

2011-10-27 Thread Dannon Baker
Hi Marc, Yes, if you change Bowtie settings to use from common to full, you'll see the entire parameter list, including Number of mismatches for SOAP-like alignment policy (-v): -Dannon On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote: Hi, is it possible to run Map with Bowtie for Illumina

Re: [galaxy-user] Amazon AMI

2011-10-31 Thread Dannon Baker
I see in your screenshot that the security group is only listed as default. Have you created the required security group as described in http://wiki.g2.bx.psu.edu/Admin/Cloud ? If so, make sure you select that security group when you launch the instance, and my guess is that it'll solve your

Re: [galaxy-user] SNPeff tool?

2011-11-08 Thread Dannon Baker
Hi Laura, While the SNPeff developers have made Galaxy wrappers available, this is not a tool we currently have installed for use on the Galaxy server at main.g2.bx.psu.edu. Off the top of my head, I don't know of any other public Galaxy servers that offer this tool, but if you have access to

Re: [galaxy-user] my data files are missing from drop down menus

2011-11-10 Thread Dannon Baker
Maya, Many tools require that fastq files specify that they are of sanger quality score. Specifically, Map with BWA for Illumina, etc. If you click the pencil icon (Edit Attributes) on your uploaded dataset and change the data type from 'fastq' to 'fastqsanger', you should be able to run

Re: [galaxy-user] [galaxy-dev] Urgent help needed

2011-12-05 Thread Dannon Baker
Toqa, Just to make sure I've understood your question: the problem is that a tool that you're trying to wrap doesn't provide a way to specify a particular output filename? Take a look at the from_work_dir attribute of a data element. Or are you asking how to define outputs in general? For

Re: [galaxy-user] [galaxy-dev] Urgent help needed

2011-12-06 Thread Dannon Baker
and I am interested in this one only ..._CNTGS_DIST0_EM20.txt any other method to overcome such problem I have presentation tomorrwo. hope things will work fine. Thank you, From: Dannon Baker [dannonba...@me.com] Sent: Monday, December 05, 2011

Re: [galaxy-user] Cucumber genome

2011-12-09 Thread Dannon Baker
Changlong, Lastz (and many other tools) allow you to select a reference from your history instead of picking one of Galaxy's built-in references. To do this, upload your reference and then when you run Lastz select in your history for the reference location, and pick your uploaded file as the

Re: [galaxy-user] Workflows Multiple datasets

2011-12-19 Thread Dannon Baker
pull -u -r 6368:de03f821784b' but it says: pulling from https://bitbucket.org/galaxy/galaxy-dist abort: unknown revision '6368:de03f821784b'! How or when can I update to the release you mentioned? Thanks, -Adhemar 2011/12/19 Dannon Baker dannonba...@me.com Adhemar, This was a bug

Re: [galaxy-user] How to add a tool to Cloud Galaxy

2012-01-07 Thread Dannon Baker
Hi Greg, In order to install custom tools you'll need to SSH into a running instance, install your tool and make any modifications to Galaxy you need in order to use it, and then use the Persist changes to file system option in the Cloudman administration panel. By default, Cloudman discards

Re: [galaxy-user] CloudMan - Galaxy - How does sharing work?

2012-01-09 Thread Dannon Baker
Greg- When you make changes to the EBS volumes of a galaxy cloudman instance and choose 'persist' from the admin panel, an EBS snapshot is taken. The next time you start an instance up, instead of creating the EBS volume from the base snapshot that we distribute, it is created from your own

Re: [galaxy-user] CloudMan - Galaxy - How does sharing work?

2012-01-09 Thread Dannon Baker
it wrong though. Also if I'm installing new libraries and programs, would those go in /mnt/galaxyTools? Thanks again, Greg On Mon, Jan 9, 2012 at 10:00 AM, Dannon Baker dannonba...@me.com wrote: Greg- When you make changes to the EBS volumes of a galaxy cloudman instance

Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

2012-01-10 Thread Dannon Baker
Data Cluster only configures a persistent data volume and SGE. Galaxy Cluster includes a running Galaxy instance in addition to the persistent data volume and SGE configuration components from the Data Cluster option. The Galaxy Cluster option is what most users will probably want to choose.

Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

2012-01-10 Thread Dannon Baker
, mailing list wrote: Thanks. So if I just want to run my own program that uses SGE, it sounds like I shouldn't need a Galaxy instance. Is that right? Does the storage space parameter control how much space is at /mnt/galaxyTools? -Greg On Tue, Jan 10, 2012 at 2:50 PM, Dannon Baker

Re: [galaxy-user] CloudMan Launch Page - Hanging

2012-01-10 Thread Dannon Baker
It looks like you're trying to restart an existing cluster (same cluster name) that previously had galaxy included. Is this the case? If so, you'll need to start it in the same availability zone as the existing volumes. On Jan 10, 2012, at 3:03 PM, mailing list wrote: The page seems to be

Re: [galaxy-user] CloudMan Launch Page - Hanging

2012-01-10 Thread Dannon Baker
permanently. -Dannon On Jan 10, 2012, at 3:18 PM, mailing list wrote: Yes, I did use the same name. I thought once I terminated everything would be gone. So how do I make a clean start? Thanks, Greg On Tue, Jan 10, 2012 at 3:08 PM, Dannon Baker dannonba...@me.com wrote: It looks like

Re: [galaxy-user] CloudMan - Persist changes to file system is not a hyperlink / clickable

2012-01-10 Thread Dannon Baker
Sorry, I should have specified before -- /mnt/galaxyData is automatically persisted, as it is assumed (and used behind the scenes in the case of a Galaxy Cluster) that this is where data will be kept. It's only /mnt/galaxyTools or /mnt/galaxyIndices that need individual flagging for

Re: [galaxy-user] CloudMan - Persist changes to file system is not a hyperlink / clickable

2012-01-11 Thread Dannon Baker
, 2012 at 4:16 PM, Dannon Baker dannonba...@me.com wrote:Sorry, I should have specified before -- /mnt/galaxyData is automatically persisted, as it is assumed (and used behind the scenes in the case of a Galaxy Cluster) that this is where data will be kept. It's only /mnt/galaxyTools or /mnt

Re: [galaxy-user] Data upload

2012-01-11 Thread Dannon Baker
Ateeq, The preferred method for uploading large files (that aren't already hosted somewhere) is FTP. See the instructions here: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP We don't generally provide specific analysis pipelines, rather the tools for composing them, though you're

Re: [galaxy-user] Login error + admin rights

2012-01-11 Thread Dannon Baker
Sarah, See the universe_wsgi.ini in your galaxy directory for configuration settings. Specifically, the admin_users section: # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the

Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

2012-01-12 Thread Dannon Baker
Yes, galaxyData is the only persistent volume you have in your data only cluster, so everything should go there. SCP should work for getting data there, unless the file is already hosted somewhere in which case wget is probably a better choice. And yes, FTP is configured specifically for

Re: [galaxy-user] Should I hg update a Galaxy Cloud ?

2012-01-12 Thread Dannon Baker
Galaxy is actually stored separately from the AMI, but the revision you'll get by default right now is:changeset: 5757:963e73d40e24date:Wed Jun 29 13:27:01 2011 -0400You can use hg directly to update galaxy, or you can use this component of the admin panel to do it:Just click update galaxy,

Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

2012-01-23 Thread Dannon Baker
?? but seems to result in 1 Megabyte. Can I set it to 1m, or 1g ? Can't see how to restart nginx yet. Thanks, Greg E On Mon, Jan 23, 2012 at 8:18 PM, Dannon Baker dannonba...@me.com wrote: Hi Greg, This is a problem with the default client_max_body_size option in nginx being

Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

2012-01-23 Thread Dannon Baker
that in my Cloud setup than instruct my (not very computer keen) wet-lab Proteomist clients how to use a subsidiary FTP package, easy though that is. But I'll try the FTP approach too for compariosn. Thanks, Greg E On Mon, Jan 23, 2012 at 8:58 PM, Dannon Baker dannonba...@me.com wrote

Re: [galaxy-user] A simple operation didn't work out

2012-02-01 Thread Dannon Baker
Hi Jiwen, The way the filter expression evaluates, you need to specify that you're matching on the string '19', and not the numerical value 19. Everything should work if you rerun with the filter condition: c1=='19' Thanks! Dannon On Feb 1, 2012, at 9:56 AM, 杨继文 wrote: Hi All, I got a

Re: [galaxy-user] The size of the history

2012-02-01 Thread Dannon Baker
Jiwen, After purging datasets, the history size update has a bit of a delay. Let us know if you find that after a while it hasn't recalculated to what you expect the value to be. -Dannon On Feb 1, 2012, at 4:21 PM, 杨继文 wrote: Hi all, First I would like to thank you for your fast replies

Re: [galaxy-user] Production environment

2012-02-10 Thread Dannon Baker
On Feb 10, 2012, at 3:28 AM, David Castillo wrote: • I haven't been able to 'Edit' Workflows like in the public server, I have been able to create them, but once I try to edit them it just attempts to load the 'Workflow Editor' but it never does. How can I solve this? Do I have to

Re: [galaxy-user] Megablast question

2012-02-16 Thread Dannon Baker
Noa has the right idea, but if you're asking for how to split a dataset into two non-overlapping halves you'll want to use Select First and Select Last, instead of random lines. Get an accurate line count from your file using the Line/Word/Character count tool and then split it right in the

Re: [galaxy-user] error uploading from ftp site

2012-03-02 Thread Dannon Baker
This should be fixed as of yesterday afternoon. Are you still having issues? -Dannon On Mar 1, 2012, at 11:28 AM, Keith E. Giles wrote: All of a sudden I can not upload any files from the FTP server. The files upload into my ftp directory fine, but when I try to upload them into galaxy,

Re: [galaxy-user] Problems starting Galaxy Cloudman

2012-03-09 Thread Dannon Baker
Greg, The problem here is that the galaxy update failed to merge a change to run.sh because of minor customizations it has. We'll have a long term fix out for this soon, but for now what you can do is ssh in to your instance and update run.sh yourself prior to restarting galaxy. All you need

Re: [galaxy-user] Cloudman - Problem starting shared cluster

2012-04-02 Thread Dannon Baker
The first thing to check would be to verify that that the bucket and contents exist in your account. Use the AWS console to log in, go to the S3 tab, and look for the bucket 'cm-31bf91279e41769ff78af22c1a276ece' and verify the /shared/2012-01-12--18-03 folder structure exists. -Dannon On Apr

Re: [galaxy-user] cuff... errors

2012-05-01 Thread Dannon Baker
There was a temporary cluster issue, but it looks like jobs are running again. Try resubmitting your jobs now, and they should succeed. -Dannon On May 1, 2012, at 8:30 PM, Jeremy Coate wrote: Hi all, FYI, I've gotten the same error recently when trying to run Bowtie (using Galaxy Main).

Re: [galaxy-user] How to transfer files between two galaxy instances

2012-05-25 Thread Dannon Baker
Hi,Just wanted to add a few clarifications here. It definitely *is* currently possible to transfer a workflow from one instance to another instance that does not have (some or all) of the tools for a particular workflow.The error you're running into "No JSON object" means that you likely have the

Re: [galaxy-user] How to transfer files between two galaxy instances

2012-05-29 Thread Dannon Baker
, considering me as a beginer. Thanks. Sorry for pushing this question. Vasu On Fri, May 25, 2012 at 11:33 AM, Dannon Baker dannonba...@me.com wrote: Hi, Just wanted to add a few clarifications here. It definitely *is* currently possible to transfer a workflow from one instance to another

Re: [galaxy-user] Galaxy in AWS AMI

2012-06-14 Thread Dannon Baker
From the log, it looks like your cluster is trying to restart from an existing instance and failing. This happens (by design) when you use the same cluster name. Can you send me the galaxy log to see where the failure might be happening? This is available at:

Re: [galaxy-user] Attempting to use parallelism in BWA

2012-07-20 Thread Dannon Baker
Hi Kevin, I'm not able to reproduce this with python 2.7. Can you confirm that galaxy is indeed using the installed python 2.7 and not, perhaps, 2.4? The structure of python's try/except/finally clause changed with python 2.5 and if you were unintentionally running 2.4 that would explain

Re: [galaxy-user] Cloudman share string not working

2012-09-18 Thread Dannon Baker
My hunch is that there's a race condition during boot that I haven't had a chance to track down and fix yet. I've actually disabled the share_string launch parameter using Galaxy's built-in cloudlaunch until this has been fixed. You can definitely still use the share string, but start the

Re: [galaxy-user] Cloudman share string not working

2012-09-18 Thread Dannon Baker
. Will the old method (entering the share string on the initial configuration dialog) be around for a while? If so I'll just tell users to do that. Thanks, Greg On Tue, Sep 18, 2012 at 9:51 AM, Dannon Baker dannonba...@me.com wrote: My hunch is that there's a race condition during boot that I

Re: [galaxy-user] Galaxy not showing my reference genome in Drop down for BowTie

2012-10-10 Thread Dannon Baker
Looking at your screenshot, you have Use a built-in index selected. If you change this to Use one from the history, do you see your fasta file listed? -Dannon On Oct 10, 2012, at 9:02 AM, greg margeem...@gmail.com wrote: Thanks Jen. But it looks like the datatype was already set to fasta.

Re: [galaxy-user] Batch jobs...

2012-10-30 Thread Dannon Baker
They were introduced and described in this news brief (with screenshots!): http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_05_20 Hope this helps, Dannon On Oct 30, 2012, at 7:33 PM, neil.burd...@csiro.au wrote: Thanks Bjorn, But I can't seem to locate the symbol/icon (looks like

Re: [galaxy-user] Batch jobs...

2012-10-30 Thread Dannon Baker
Ahh, I see what's going on. Galaxy relies on the Input Dataset step for this feature. If you use these in your workflow, Galaxy will be able to perform the batch execution. Find them in the workflow editor under Workflow control - inputs. -Dannon On Oct 30, 2012, at 8:46 PM,

Re: [galaxy-user] Batch jobs...

2012-10-30 Thread Dannon Baker
d 3 as its not connected on the workflow diagram? Neil-Original Message-From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Wednesday, 31 October 2012 10:54 AMTo: Burdett, Neil (ICT Centre, Herston - RBWH)Cc: bjoern.gruen...@pharmazie.uni-freiburg.de; galaxy-user@lists.bx.psu.eduSubject: R

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Dannon Baker
Can you describe more about what is broken with your cloud install? Regarding main - the server has been under heavy load today and, while it shouldn't remain frozen, might be slow to dispatch and, depending on the type, execute) jobs. -Dannon On Nov 7, 2012, at 1:12 PM, Larry Reiter

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Dannon Baker
- and me - could not go any further (i.e. jobs are grey and never start to run). Class ended almost three hours ago. Does this help? LTR On 11/7/12 2:52 PM, Dannon Baker wrote: Can you describe more about what is broken with your cloud install? Regarding main - the server has been

Re: [galaxy-user] Teaching GALAXY

2012-11-08 Thread Dannon Baker
wrote: It looks like both the main server and our local install are frozen. Nothing has run since we started yesterday at about 11:30am. Anybody know why? LTR On 11/7/12 4:05 PM, Dannon Baker wrote: Main will complete the jobs eventually, though obviously that's not particularly useful

Re: [galaxy-user] tophat

2012-11-09 Thread Dannon Baker
It isn't normal, but this can happen during periods of extremely high load like we're currently experiencing. If you leave your jobs in the queue, they'll execute as soon as possible - don't cancel or restart your jobs as this will only move them to the back of the queue and delay completion.

Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Dannon Baker
be receptive to some help, so you should mail him. LTR On 11/7/12 4:05 PM, Dannon Baker wrote: Main will complete the jobs eventually, though obviously that's not particularly useful in the context of your class today. How is your cloud instance set up? Cloud or local instances should

Re: [galaxy-user] Galaxy server configuration - what is [server:main]?

2012-11-16 Thread Dannon Baker
That's just the section demarcation stating that everything following (until the next such bracketed line) is a property of the 'server:main' section -- there should be no need to change that, though you can certainly change any of the properties within the section as needed. -Dannon On Nov

Re: [galaxy-user] question on galaxy reference genome window

2012-12-19 Thread Dannon Baker
Kathryn, Are you using the galaxy cloud configuration provided by the team, or have you installed your own galaxy on a cloud instance? It sounds like the latter, in which case you'll need to configure reference as detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You

Re: [galaxy-user] [External] Re: question on galaxy reference genome window

2012-12-19 Thread Dannon Baker
On Dec 19, 2012, at 11:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: I also have the preconfigured cloud instance set up recently. However, when I stopped the instances (master and cluster nodes) from aws, I couldn't get the galaxy web running again (the instance running however the

Re: [galaxy-user] galaxy cloudman login and aws instance

2012-12-20 Thread Dannon Baker
It looks like you've worked on both the public galaxy site we provide (main.g2.bx.psu.edu) and your own cloud instance. Data on the public instance won't be automatically migrated to the cloud instance and vice versa. All work done on the cloud site will remain there and persist after

Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

2012-12-20 Thread Dannon Baker
] sun_wenp...@bah.com wrote: Thanks and my question is-- How to shutting down the cloud if working on main.g2.bx.psu.edu? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:38 PM To: Sun, Wenping [USA] Cc: galaxy-u

Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

2012-12-20 Thread Dannon Baker
the cloud if working on main.g2.bx.psu.edu? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Thursday, December 20, 2012 1:38 PM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] galaxy cloudman login

Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

2012-12-20 Thread Dannon Baker
On Dec 20, 2012, at 2:33 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: Thank you very much for the information. For the last part of using ec2 instances at aws, is there an option that I can control galaxy's operation at aws site? This way I can start/stop the instance when I need. I

Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

2012-12-20 Thread Dannon Baker
On Dec 20, 2012, at 2:52 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: The problem is that if use usegalaxy.org/cloudlaunch to restart galaxy, it will launch to main.g2.bx.psu.edu, where I have no control on the data security and running queues. Meanwhile, the correspondingly initiated

Re: [galaxy-user] [External] Re: galaxy cluster nodes from the cloudlaunch site

2012-12-27 Thread Dannon Baker
In the main (non-admin) cloudman UI you'll see a little icon next to the volume size. Click this and you'll have the opportunity to enter a new size. Upon submitting this, galaxy will need to temporarily shut down, but it should be automatically restarted once the procedure is complete. Note

Re: [galaxy-user] galaxy cloudman login

2013-01-02 Thread Dannon Baker
To be clear, your admin user still works on this instance but another one does not? If this is the case, can you log in as the admin user (and, if not, simply register a new user and make it an admin) and take a look at the user list in the admin panel? To get to the user list when in Galaxy,

Re: [galaxy-user] [External] Re: galaxy cloudman login

2013-01-02 Thread Dannon Baker
On Jan 2, 2013, at 5:17 PM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: 1. how to retain my previous work? If you were logged in when you were working previously, we just have to figure out who you were logged in as, and log back in. You may also want to check Saved Histories to make sure

Re: [galaxy-user] [galaxy-dev] Workflows

2013-01-18 Thread Dannon Baker
Geert, this is great stuff! One small correction -- the API is enabled by default as of revision 7022:8376ad08ae41 (April 2012). -Dannon On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer geertvandewe...@gmail.com wrote: Hi, I've put together some exempels for activating and using the api.

Re: [galaxy-user] gather results from multiple histories

2013-02-01 Thread Dannon Baker
Hey Mark, Yep, sure can. Just click on the gear in the history panel and go to Copy Datasets, and copy those datasets you're interested in to th specific new history you want to use. -Dannon On Feb 1, 2013, at 10:15 AM, mark.r...@syngenta.com wrote: Hi All Let’s say that I have results

Re: [galaxy-user] Galaxy on one computer not showing latest runs in history

2013-02-13 Thread Dannon Baker
Dikla, After refreshing the browser, the most up-to-date view of the history should definitely be available. Are you positive you're looking at the same history in both places? I would verify that there's nothing in Saved Histories that looks like what you're expecting. -Dannon On Feb 13,

Re: [galaxy-user] Welcome to the galaxy-user mailing list (Digest mode)

2013-02-20 Thread Dannon Baker
Of course! Any subscriber can post -- it looks like your message Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file went through correctly. Thanks for your interest. -Dannon On Wed, Feb 20, 2013 at 11:36 AM, Bodour Al-Khamees alkhameesbod...@gmail.com wrote: Hello, I

Re: [galaxy-user] fastq quality trimmer

2013-04-17 Thread Dannon Baker
Hi Tomaž, The script depends on galaxy libraries, but could probably be set up standalone if you made the appropriate libraries available -- the source is distributed with galaxy, see https://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastq/fastq_trimmer_by_quality.py?at=default -Dannon

Re: [galaxy-user] Downloading files via FTP

2013-05-07 Thread Dannon Baker
No, currently HTTP is the only way to download files from Galaxy. -Dannon On Tue, May 7, 2013 at 4:22 AM, lilach noy lilach...@gmail.com wrote: Is it possible? If so, how? Thank you, Lilach ___ The Galaxy User list should be used

Re: [galaxy-user] receiving an email when a processing step finishes

2013-05-17 Thread Dannon Baker
Actually, you can do this in workflows out of the box in Galaxy (as long as your instance is configured to send mail). All you need to do is edit the workflow, select the step you want to be notified following, and add a Step Action- Email Notification. On Fri, May 17, 2013 at 9:41 AM, Geert

[galaxy-user] Fwd: galaxy on the cloud

2013-06-03 Thread Dannon Baker
Hi Alejandro, It should show up if you search for the AMI ID, which is ami-da58aab3. That said, the easiest way to launch a galaxy cloud cluster if you're not already familiar with EC2 is probably using usegalaxy.org/cloudlaunch. This interface will guide you through the launch process without

Re: [galaxy-user] problem with custom database build

2013-06-11 Thread Dannon Baker
Hi Ann, My guess is that this is related to the issue you were having before. I'm taking a look now. -Dannon On Mon, Jun 10, 2013 at 7:31 PM, Ann Holtz-Morris, M.S. aholtzmor...@chori.org wrote: Hi, I’m trying to create a new custom build . I keep getting *GURU MEDITATION:

Re: [galaxy-user] galaxy-user Digest, Vol 86, Issue 17

2013-08-21 Thread Dannon Baker
Hi Jun, Thanks for the clarification. Workflow step annotations would best suit your needs, I think. When you're in the editor, click on any step and on the right side you'll see a field Annotation / Notes which will be displayed when the workflow is viewed. This can be used to clear up any

Re: [galaxy-user] cloudman console not responding add/remove nodes

2013-08-25 Thread Dannon Baker
On Sun, Aug 25, 2013 at 3:35 PM, Deniz Erezyilmaz deniz...@gmail.comwrote: When I try to add nodes from the galaxy console, they never register as available and the icons never switch from blue to yellow to green. The cluster status log shows that they have been added. However, when I try to

Re: [galaxy-user] Error out of memory when trying to retrieve output

2013-08-29 Thread Dannon Baker
Do you have debug enabled in your universe_wsgi.ini? IIRC, this causes the entire request to be loaded into memory (which is a bad thing when the response is 20GB). On Thu, Aug 29, 2013 at 3:50 PM, Delong, Zhou delong.z...@usherbrooke.cawrote: Hello, I wanted to download the accepted

Re: [galaxy-user] Need your helps about Galaxy

2013-09-26 Thread Dannon Baker
Sorry for not being able to take a look at this sooner, thanks for figuring it out and posting back! This one must have fallen through the cracks when we updated all the paths with the last Cloudman release, I'll make a note to fix it with our next minor update. -Dannon On Thu, Sep 26, 2013 at

Re: [galaxy-user] galaxy cloud: location of imported and converted fastq's

2013-10-07 Thread Dannon Baker
Hi PT, What exactly do you mean by Galaxy on the Cloud appears to expect that the imported and converted fastq files are in the same S3 bucket where the fastq.gz files were? Once imported from S3, you're correct in that everything will be on the local EBS volume. -Dannon On Sun, Oct 6, 2013

Re: [galaxy-user] How to lauch bulit cluster on Cloudman?

2013-10-08 Thread Dannon Baker
That means that the galaxy instance for your cluster didn't start. It probably should have. Can you send me (directly, without the list -- it can contain sensitive info) the cloudman log from the admin panel? -Dannon On Tue, Oct 8, 2013 at 9:17 AM, Yan He yanh...@hotmail.com wrote: Dear

Re: [galaxy-user] Need your helps about Galaxy

2013-10-09 Thread Dannon Baker
Can you send me the more detailed full cloudman log from the admin interface (it may be quite large). This will help me see what may have happened. On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan leiyan2...@gmail.com wrote: Hi all, I found some very strange problems on our cloud Galaxy (

Re: [galaxy-user] Need your helps about Galaxy

2013-10-09 Thread Dannon Baker
and Translational Genomics The University of Tennessee Health Science Center On Wed, Oct 9, 2013 at 4:04 PM, Dannon Baker dannon.ba...@gmail.comwrote: Can you send me the more detailed full cloudman log from the admin interface (it may be quite large). This will help me see what may have happened

Re: [galaxy-user] inconsistant error messages on disk quota?

2013-10-28 Thread Dannon Baker
Hey Francis, There's a bug in the current release of cloudman that causes files fetched by galaxy (this doesn't affect direct http or ftp upload) to use the root volume as temporary storage, which has very little space. This is fixed in the next release scheduled to coincide with the

Re: [galaxy-user] Grouping Histories into related Projects

2013-11-01 Thread Dannon Baker
The right approach here is probably to use history tags (at the top of a history panel, click the tag icon just below the history name). You could tag several histories with a particular sample name, organism, etc. While you can *search* for histories by tags and get a list of, say, all Mouse

Re: [galaxy-user] Importing workflow from file fails in Galaxy instance on Amazon Cloud

2014-01-06 Thread Dannon Baker
Sébastien, This seems to be a galaxy bug from a little while back. To fix your cloud instance, go to the cloud admin console and click Update Galaxy, and the problem should be resolved once galaxy updates and restarts. -Dannon On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau

Re: [galaxy-user] Installing tool in galaxy on cloud

2014-02-03 Thread Dannon Baker
After adding yourself as an admin in Cloudman, your galaxy instance restarted, correct? If so, can you double check that the cloudman admin interface indicates your exact email address that you've logged into galaxy as? -Dannon On Mon, Feb 3, 2014 at 12:32 PM, Malik, Shivani

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