Re: [galaxy-dev] ENA SRA data retrieval with Cloudman

Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Wed, Apr 2, 2014 at 6:21 PM, Dannon Baker wrote: > On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian wrote: > >> Hi Dannon, >> Thanks for this information. Will the ENA SRA button be enabled on the >> next update

Re: [galaxy-dev] ENA SRA data retrieval with Cloudman

so my guess is that this tool was > unintentionally removed when we last updated the volume. It's actually > still available on disk, though, and can be re-enabled in your > tool_conf.xml by adding the following back to your Get Data section: > > > > -Dannon > >

[galaxy-dev] ENA SRA data retrieval with Cloudman

Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144a) that there is no option to "Get Data" from the ENA SRA. We've found that retrieving large (fastq) data sets from public database

Re: [galaxy-dev] Installing DeepTools on Cloudman 2.0

wrote: > Am Dienstag, den 03.12.2013, 16:19 -0500 schrieb Mohammad Heydarian: > > Hi Bjorn, > > Thanks for the quick response. > > > > > > I am running version: 10201:ebe87051fadf, when I updated to the latest > > version, I was able to start the install of Dee

Re: [galaxy-dev] Installing DeepTools on Cloudman 2.0

Hi Bjorn, Thanks for the quick response. I am running version: 10201:ebe87051fadf, when I updated to the latest version, I was able to start the install of DeepTools. The tool seemed to be installing but when I went to refresh the page, I was greeted with this message: "Initializing repository in

[galaxy-dev] Installing DeepTools on Cloudman 2.0

Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error: Internal Server ErrorGalaxy was unable to

[galaxy-dev] Cloudman database issue (?)

Hello, I found a couple of issues in using the latest version of Cloudman (revision:10201:ebe87051fadf"). The "Extract Genomic DNA" tool returns an error: "No sequences are available for 'mm9', request them by reporting this error." Upon trying to report the error in Galaxy (on the page that come

Re: [galaxy-dev] [galaxy-user] Connecting to new Galaxy Cloudman by FTP

4:22 PM, Nate Coraor wrote: > On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote: > > > Hi, > > I am having trouble setting up a FTP connection with the recently > released version of Galaxy Cloudman (ami-118bfc78). > > > > I have instantiated the new version

Re: [galaxy-dev] Galaxy CloudMan release - Tophat does not work

Cufflinks, Cuffcompare, and Cuffdiff are also failing to run because they can not be found. I am using the newly released version of Cloudman 2.0 ( ami-118bfc78). Any help would be appreciated. Cheers, Mo Heydarian On Mon, Jul 8, 2013 at 5:02 PM, Ravpreet Setia wrote: > Some tools (tophat is

[galaxy-dev] Connecting to new Galaxy Cloudman by FTP

Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group set

[galaxy-dev] Exporting Trackster visualizations.

Hi, Is there a way to export visualizations from Trackster and Sweepster in .pdf or .jpg format? I have been using these fantastic tools to fine tune my parameters and would like to show how I did so in figure format (partially to locally get the word out about these powerful tools). Screenshots of

Re: [galaxy-dev] Empty TopHat output

ing a new instance. > > Try using the admin console to update to the most recent Galaxy dist using > this URL: > > https://bitbucket.org/galaxy/galaxy-dist/ > > (not galaxy-central, as is the default) > > Best, > J. > > On Oct 31, 2012, at 8:36 PM, Mohammad Heyda

Re: [galaxy-dev] Empty TopHat output

ed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks wrote: > Given that this doesn't seem to be happening on our public server or on > local instances, my best guess is that the issue is old code. Are you > running the most recent dist? > > J. > > > On Oct 31, 2012, at 7:37 P

Re: [galaxy-dev] Empty TopHat output

We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is "empty" files. Is anyone else having this issue? Does anyone have any suggestion

Re: [galaxy-dev] Empty TopHat output

We have been having also been having this issue, we get empty TopHat output files. This is happening on two instances that were started within the past three weeks on the cloud. Cheers, Mo Heydarian -- Forwarded message -- From: 吳正華 Date: Fri, Oct 12, 2012 at 11:12 PM Subjec

[galaxy-dev] Blastxml error on Galaxy Cloudman

Hello, I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I have since not been able to run any jobs. I get the following error: WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.data

Re: [galaxy-dev] Error in loading tools.

t; /cloud/admin/) to the latest version. > > -Dannon > > On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian > wrote: > > > Hi Galaxy Community! > > Hope all is well. > > > > I've been trying to install some tools in my Galaxy Cloudman instance > (usi

[galaxy-dev] Error in loading tools.

Hi Galaxy Community! Hope all is well. I've been trying to install some tools in my Galaxy Cloudman instance (using image: ami-da58aab3 ) from the main toolshed. When I try to "install to local Galaxy" I get the error: Not Found The resource could not be found. No action for /admin_toolshed/pre

[galaxy-dev] Trackster - not showing data.

Hi, I have been trying to use trackster on the main Galaxy server for a couple of days now. It was working fine for me early yesterday, I was looking at (larger) BAM files, then it just stopped and would not display the data of the loaded tracks (but did display the track title). I have tried to st

Re: [galaxy-dev] Can't upload Cuffmerge files to Galaxy Cloudman

Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Thu, May 3, 2012 at 8:19 AM, Mohammad Heydarian wrote: > Hello, > I can not upload Cuffmerge files to Galaxy Cloudman. I can load othe

[galaxy-dev] Can't upload Cuffmerge files to Galaxy Cloudman

Hello, I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf files just fine, but not the "merged transcripts.gtf" file from Cuffmerge. This is the first time this has happened. After I upload my "merged transcripts.gtf" file (via ftp) I can not move the file to the history pa

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

Great idea. In! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein < annbl...@eng.uiowa.edu> wrote: > Hi everyone - > > Here at the

[galaxy-dev] Increasing EBS storage above 1TB for use with Galaxy cloudman.

Hello, I am performing NGS data analysis using Galaxy cloudman. I am working with very large Fastq files that add up and approach the 1TB limit of the EBS volume when I perform my analysis. Is there a way to use multiple EBS volumes with one EC2 instance of Galaxy cloudman. For example, could I dir

[galaxy-dev] Private key file format issue (for connecting EC2 instance with EBS volume)

Hello, I am trying to connect an EC2 instance to an EBS volume. I have attached the EBS volume to the EC2 instance (running Galaxy). I now need to mount the EBS volume to the EC2 instance. To do this I will use Putty to make the connection. But first I have to convert the private key from ".pem" f

[galaxy-dev] How do you connect existing EBS volumes to a fresh EC2 instance?

Hello, How do you connect existing EBS volumes to a fresh EC2 instance on Amazon? I have been starting the EC2 instance and choosing "test cluster" where the option to use EBS volume space is given (when the Galaxy cloud console starts up), since there is no place to insert my EBS volume address.

[galaxy-dev] Moving data about the EC2/EBS/S3 spaces on the Amazon cloud.

Hello, I am new to cloud computing and am trying to use the Galaxy cloudman service through Amazon to analyse NGS data. I have a couple of questions regarding data transfer: If I am running an EC2 instance, with an EBS volume attached, how can I retrieve the data from the EBS volume? In addition,