[galaxy-dev] upgrading a local local galaxy server - was: Error trying to remove trackster visualization in latest galaxy-dist

Hi Thon, James and Dannon I fully understand Thon's frustration. I have been running into similar situations during code upgrades of our production server. Although the code is tested on 'Galaxy main', it is rather impossible to catch everything, since most local Galaxy servers have a differe

Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy

Thanks! This looks very useful for me. I'm also interested in fleshing out the wrapper, (implementing all possible options, like bowtie's <>), but this should fit my purposes for now. Best regards, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:

[galaxy-dev] Tool Error or Bug?

Hi, I cannot determine if I have a tool error or a bug and I am getting errors when I try to report the problem so I am not sure where to send a request for help. I hope i have directed this to the correct place for assistance. I have used Galaxy's main web tools many times successfully so I am f

[galaxy-dev] local install problem with fasta manipulation tools?

Hi I hope I have the correct place to ask for assistance. I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told "No such file or directory /bin/sh: fasta_forma

Re: [galaxy-dev] Workflows

Hi, I've put together some exempels for activating and using the api. You can find them here: http://geertvandeweyer.zymichost.com/index.php?page=read&id=29 Best regards, Geert vandeweyer Op 16-jan.-2013 om 02:52 heeft het volgende geschreven: > Hi >Sorry if these questions are obvio

[galaxy-dev] Problem uploading to Galaxy

Hello, I've encountered a problem uploading some .xlsx files to Galaxy. None of the files I've tried uploading today, via html or ftp, have been successfully uploaded. Instead, the box turns grey and says the "Job is waiting to run." If I try to refresh, I get the error: The 'Upload File' tool doe

[galaxy-dev] Fwd: Number of SNPs

Dear Galaxy Team We recently bagan to use galaxy in our lab. I uploaded the whole SNPs several times but the number of them showed difference in every time . Would you please do me a favor and let me know why the number of SNPs differ in every times and what is the reason of this? Best regards,

[galaxy-dev] Galaxy Main cloudlaunch stall

I've searched the list to see if anyone specifically mentions not being able to use the "cloud launch" feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user

[galaxy-dev] UCSC Data Browser

Hello, Is anyone having trouble with the UCSC data browser? I got the following from one of my users: Hi guys, I try to fetch data from UCSC browser. A summary of my query shows that I am getting what I ask for, but when I "Send the data to Galaxy" I am returned to the channing galaxy home page a

Re: [galaxy-dev] Galaxy Main cloudlaunch stall

Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that s

Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy

Do you know how I can read in gzipped FASTQ files in the STAR wrapper without writing an external Python script or the like? Thanks, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cs

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

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 wrote: > Hi, > > I've put together some exempels for activating and using the api. You can > find them her

Re: [galaxy-dev] missing eye icon on running jobs…

The display icon has been re-enabled in revision 8634:b9d44cf4b68e. Thanks for the catch/feedback. On Wed, Jan 9, 2013 at 12:00 PM, Langhorst, Brad wrote: > In some cases (e.g. mira) it's nice to be able to follow what's going on > in the log file… > > Does anybody else miss being able to vi

Re: [galaxy-dev] missing eye icon on running jobs…

On Wed, Jan 9, 2013 at 5:00 PM, Langhorst, Brad wrote: > In some cases (e.g. mira) it's nice to be able to follow what's going on in > the log file… > > Does anybody else miss being able to view files as they're running? > > brad I remember specifically testing that I could read MIRA's log in Gal

Re: [galaxy-dev] Galaxy Main cloudlaunch stall

Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker wrote: > Cloudlaunch on the main public instance is fully supported

[galaxy-dev] galaxy using EC2 spot pricing

Does anyone have any experience running Galaxy using Amazon's EC2 spot pricing? It seems like that could save a lot of money as compared to on-demand pricing, and it appears that there are ways to mix on-demand and spot instances within one processing cluster: http://aws.amazon.com/ec2/spot-and-sc

Re: [galaxy-dev] galaxy using EC2 spot pricing

While it isn't bulletproof yet (restarting jobs that fail due to spot instance reclaims, etc), Cloudman (usegalaxy.org/cloud) does currently have support for running worker nodes as spot instances. When you go to add nodes, just click "Use Spot Instances", and add your spot price. For obvious

Re: [galaxy-dev] Problem uploading to Galaxy

Hi Andrew, If this was on Main at Penn State, there was a problem with uploads that we believe has now been resolved. Dave C On Wed, Jan 16, 2013 at 5:21 PM, Andrew Gorzalski wrote: > Hello, > > I've encountered a problem uploading some .xlsx files to Galaxy. None of > the files I've tried uplo

Re: [galaxy-dev] Galaxy Main cloudlaunch stall

Should definitely be stable enough to use in a classroom and that it isn't working for you is definitely unexpected; it's the only way I've launched instances for many months now. I'm digging through logs to see if I can find any indication of why your particular requests are having issues.

[galaxy-dev] login problems

Hello, I am trying to connect to ftp with my username and password that I registered in galaxy. I am doing this through Filezilla. I am getting the error "could not connect to server". Do you know what the problem is, please? Thank you. Eleanne

[galaxy-dev] Colon in drmout and drmerr file names creates issues with Torque and DRMAA when using 'use_tasked_jobs'.

Hi All, Thanks to this email[1] from Peter Cock I was able to find what was causing the error I initially described here[2]. I also now have a theory of why this is happening. My unconfirmed guess. When a colon is present in the standard output or standard error file, someone betweent Galaxy, pyt

Re: [galaxy-dev] local install problem with fasta manipulation tools?

> I hope I have the correct place to ask for assistance. Yes, this list is a great place to ask questions about local Galaxy instances. > I've been trying to use a local install of Galaxy. I can upload data and > convert formats (FASTq to FASTA) but can't use fasta manipulation tools like > wid

Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy

The wrapper isn't set up to support gzipped FASTQ because Galaxy unzips datasets when they are uploaded, so the wrapper won't ever see a gzipped FASTQ dataset. We plan to dataset gzip support to Galaxy in the future. J. On Jan 18, 2013, at 10:21 AM, Sorn, Patrick wrote: > Do you know how I can

Re: [galaxy-dev] Galaxy Main cloudlaunch stall

Thanks for the response. I'll try again today. The browser I'm using is Safari 6.0.2 on Mac OS 10.8.2. On Jan 18, 2013, at 10:17 AM, Dannon Baker wrote: > Cloudlaunch on the main public instance is fully supported and should work > fine -- I use it regularly for launching instances without i

Re: [galaxy-dev] Galaxy Main cloudlaunch stall

Thanks. The requests will be coming from kennedykrieger.org. On Jan 18, 2013, at 12:36 PM, Dannon Baker wrote: > Should definitely be stable enough to use in a classroom and that it isn't > working for you is definitely unexpected; it's the only way I've launched > instances for many months n

Re: [galaxy-dev] Galaxy Main cloudlaunch stall

Thanks, Quang. That's not exactly what I'm looking for. My motivation is to teach an entire class how to start a Galaxy cluster on their own, with minimal knowledge of AWS or systems administration. The "cloudlaunch" feature on the main psx site seems to fit this purpose exactly, but does not wo

Re: [galaxy-dev] Bug in handling user job limits (due to dynamic job runner code?)

Just an update on this issue. Upon further investigation, it looks like the dynamic job runner code in commit 6f3b4e8 broke this. I haven't been able to parse through everything going on yet to propose a fix, but I've discovered two things: 1) Moving the self.__clear_user_job_count() call outs

Re: [galaxy-dev] login problems

Hi Eleanne, Take a look at http://wiki.galaxyproject.org/FTPUpload. FTP also needs to be enabled on the Galaxy server you are using. Which server are you trying to connect to? Thanks, Dave C. On Fri, Jan 18, 2013 at 10:42 AM, Solorzano, Eleanne < eleanne.solorz...@unh.edu> wrote: > Hello