Re: [galaxy-user] Mapping does not start

2011-02-15 Thread Nate Coraor
Felix Hammer wrote: Hi, I am trying to map sequences with Bowtie. Have been waiting for a few hours now but it still says Job is waiting to run. A few days ago I didn't have this problem and the job started immediately. My guess is that the jobs are still stuck in a queue? How can I

Re: [galaxy-user] Upload via SCP?

2011-02-17 Thread Nate Coraor
Felix Hammer wrote: Hi, is it possible to use SCP to upload files instead of FTP? Hi Felix, At this time, no. --nate thxbye, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] Bowtie Job doesn't start

2011-03-07 Thread Nate Coraor
Felix Hammer wrote: Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Hi Felix, It looks like the reservation on the cluster which runs bowtie jobs isn't working at the moment and there's some contention for resources. I've

Re: [galaxy-user] Export data to filesystem

2011-03-15 Thread Nate Coraor
James Lindsay wrote: Hello, I was wondering if there was a way to export a dataset to the file system? Basically I think it would be advantageous if someone could copy a dataset to an export folder, they could then FTP this data away or work with it locally? Hi James, This doesn't exist

Re: [galaxy-user] Galaxy down?

2011-03-21 Thread Nate Coraor
Felix Hammer wrote: Hi, is there currently a problem with the Galaxy Server? When will it be up again? Hi Felix, There were some problems caused by unusually high load which should now be resolved. Jobs are running now, albeit a bit slowly. Please let us know if there are any continuing

Re: [galaxy-user] Galaxy server-FTP

2011-03-31 Thread Nate Coraor
Sher, Falak wrote: HI I would like to use Galaxy server to upload files via FTP. I seek help for, log in to the FTP server at main.g2.bx.psu.edu. I dont see ftp log in option there. help please ? Hi Falak, What software are you using to try to connect via FTP? --nate Falak

Re: [galaxy-user] Galaxy server-FTP

2011-04-01 Thread Nate Coraor
-platform FTP client. --nate From: Nate Coraor [n...@bx.psu.edu] Sent: Thursday, March 31, 2011 11:36 PM To: Sher, Falak Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Galaxy server-FTP Sher, Falak wrote: HI I would like to use Galaxy

Re: [galaxy-user] Reload .loc files without restarting the Galaxy server?

2011-04-21 Thread Nate Coraor
Roman Valls wrote: On standard UNIX, the SIGHUP signal (kill -HUP PID) is used to perform this kind of actions (re-read config files) on almost all daemons [1]. Doing a quick grep: $ grep -ri HUP galaxy-central Nothing shows up, so as Jen indicated, does not seem to be implemented at

Re: [galaxy-user] runtime warning with pysam egg

2011-04-29 Thread Nate Coraor
Shantanu Pavgi wrote: Hi, I am getting following warning when I start the galaxy server. I am using latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the configuration here? {{{ $ ./run.sh

Re: [galaxy-user] suggestion for multithreading

2011-06-02 Thread Nate Coraor
Hi Louise-Amélie, I haven't done anything with this code yet, but I wanted to let you know that we'll eventually be adding it, I'm just going to change the implementation slightly. I'd like to merge the functionality of the csv into an xml config I'm already working on (but haven't yet fully

Re: [galaxy-user] suggestion for multithreading

2011-06-02 Thread Nate Coraor
Peter Cock wrote: 2011/6/2 Nate Coraor n...@bx.psu.edu: Hi Louise-Amélie, I haven't done anything with this code yet, but I wanted to let you know that we'll eventually be adding it, I'm just going to change the implementation slightly.  I'd like to merge the functionality of the csv

Re: [galaxy-user] Most Popular Linux flavour for Galaxy

2011-06-07 Thread Nate Coraor
Matloob Khushi wrote: Hello Galaxy Users We are anticipating setting up a local instance of Galaxy and wondering what is the most popular (or best) flavour of Linux people out there using. I wonder which OS on UseGalaxy.org has been used. Thanks for your help. Hi Matloob, The public

Re: [galaxy-user] Loading files to local Galaxy

2011-06-07 Thread Nate Coraor
Paul-Michael Agapow wrote: From: Tilahun Abebe tilahun.ab...@uni.edu We are trying to load Illumina data to our local Galaxy instance. The files are between 700 MB and 2.2 GB. Files below 2 GB load in less than 5 minutes. Files larger than 2 GB don't upload at all. We installed

Re: [galaxy-user] Loading files to local Galaxy

2011-06-07 Thread Nate Coraor
. Has anyone tried this before? Yes, this is a standard feature. zip, gzip, and bzip2 are all supported. Only one file per archive at this time, however. --nate Thanks. Tilahun --- Nate Coraor wrote: Paul-Michael Agapow wrote: From: Tilahun Abebetilahun.ab...@uni.edu We

Re: [galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw

2011-06-09 Thread Nate Coraor
Hello, Please don't set your bug report address (error_email_to in universe_wsgi.ini) to the user mailing list. This should be set to a local address at your site. --nate galaxy-user@lists.bx.psu.edu wrote: GALAXY TOOL ERROR REPORT This error report was sent

Re: [galaxy-user] uploading files via FTP

2011-06-13 Thread Nate Coraor
somy ork wrote: Hi, Am trying to configure galaxy to enable file upload via FTP. My server is configured with SFTP. and not FTP. Will this create a problem in galaxy? coz all my input files are above 2 GB. Should i change any settings in the universe_wsgi.ini file? Please guide me. Hi

Re: [galaxy-user] SRMA on a local galaxy instance?

2011-06-16 Thread Nate Coraor
Gong, Henry wrote: Does anyone know how to get SRMA to work properly in galaxy? I've used the pre-built 0.1.15 jar as well as a 0.1.16 jar I built from source, but the result of an SRMA re-alignment job in both instances is a python process which only takes a few percent CPU (or less,

Re: [galaxy-user] galaxy cluster setup

2011-06-16 Thread Nate Coraor
Robert Jackson wrote: Does anyone have practical info on galaxy setup on a cluster? Hi Robert, Please see the production server documentation at: http://usegalaxy.org/production --nate Robert C. Jackson Software Systems Specialist III The University of Texas Pan-American Computer

Re: [galaxy-user] Galaxy server issues?

2011-06-17 Thread Nate Coraor
David K Crossman wrote: Hello! We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to Get Data and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked Excecute. The 12 moved

Re: [galaxy-user] cuffcompare error in galaxy

2011-06-20 Thread Nate Coraor
Hi Carlos, We're expecting to release a stable distribution this week, but you are always free to pull changes from the central repository. The suggested method would be to just pull all changesets up to the one you want, or up to the tip changeset. It's not trivial to pull single changesets,

Re: [galaxy-user] Unable to load FASTA files?

2011-06-27 Thread Nate Coraor
Hi, The cluster resource manager unexpectedly died. Everything should be working again after a restart. Please let us know if you're still experiencing any problems, and thanks for using Galaxy. --nate Nicola Nadeau wrote: I've been getting the same error when trying to run Picard, Mark

Re: [galaxy-user] FTP and command line access in Galaxy

2011-06-28 Thread Nate Coraor
Peter Cock wrote: On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson curt...@uab.edu wrote: Nate, The Galaxy’s ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with

Re: [galaxy-user] [galaxy-dev] input security validation

2011-06-28 Thread Nate Coraor
Roman Valls wrote: Sorry for the cross-posting, but I guess that's also interesting to Galaxy users... I've been thinking about input validation too... only a bit more generally, on a server/production basis. Nate, on your production setup[1] (galaxy main), do you use any kind of filter or

Re: [galaxy-user] temporary files

2011-06-28 Thread Nate Coraor
Christopher Schroeder wrote: Dear all, we extended the galaxy functionality with a couple of smaller custom scripts. Now we are in the need of some tmpFiles, since our data is getting bigger. As far as I understand galaxy by now there might be several options: - job_working_directory

Re: [galaxy-user] Galaxy Architecture Documentation

2011-09-23 Thread Nate Coraor
Oren, I do believe some folks have done this, I am a bit surprised none have replied. But yes, since Condor supports DRMAA, you should be able to point $DRMAA_LIBRARY_PATH at Condor's libdrmaa.so, enable the drmaa runner, and try it out. --nate Oren Livne wrote: Dear Dave, Victor, Is it

Re: [galaxy-user] Injecting External File References

2011-09-27 Thread Nate Coraor
Oren Livne wrote: Dear All, We have a lot of sequencing data files whose locations and identifiers are managed by our home-grown webapp. We'd like to enable users to single-sign-on from our webapp into Galaxy (we will be using open ID on both systems for that). When the user opens a Galaxy

Re: [galaxy-user] reducing size on disk to comply with quotas

2011-10-26 Thread Nate Coraor
Patrick Kenneth Gonzales wrote: Hi, I am currently using 636gb of storage and would like to reduce it. I have deleted (from disk) most of the datasets in my history. All I've kept are the Bam files which are around 2.7gb each . Unfortunately, the size on Disk reads 448.5gb in my saved

Re: [galaxy-user] Over disk quota

2011-10-26 Thread Nate Coraor
GANDRILLON OLIVIER wrote: Hello I just received the following message while using Galaxy through the web You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. I deleted a couple of files but it didn't helped. I checked the FAQ

Re: [galaxy-user] permanently delete problem

2011-10-26 Thread Nate Coraor
Richard Mark White wrote: hi,   so i went to options--saved history--advanced--deleted datasets.  then checked all of them, and then hit permanently delete. but nothign happened.  they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich Hi

Re: [galaxy-user] permanently delete problem

2011-10-26 Thread Nate Coraor
Great, thanks for letting us know. Richard Mark White wrote: actually, i just waited a bit and now they are deletd. r From: Nate Coraor n...@bx.psu.edu To: Richard Mark White whit...@yahoo.com Cc: GANDRILLON OLIVIER olivier.gandril...@univ-lyon1.fr

Re: [galaxy-user] Data gets deleted from public server

2011-11-07 Thread Nate Coraor
On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote: I uploaded two BAM files and was working with them but when I tried to use them again they are automatically deleted along with all the steps of analysis? Any reason or I am missing something. Hi Shamsher, Were you logged in when you

Re: [galaxy-user] Lastz

2011-11-11 Thread Nate Coraor
On Nov 11, 2011, at 9:21 AM, Andrew South wrote: Hello folks Anyone else having trouble with running Lastz to map? Jobs are being sent but not running. It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. Hi Andy, It

Re: [galaxy-user] Lastz

2011-11-11 Thread Nate Coraor
Galaxy, --nate Please consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 14:55 On Nov 11, 2011, at 9:21 AM, Andrew South wrote: Hello folks Anyone else having

Re: [galaxy-user] Lastz

2011-11-14 Thread Nate Coraor
consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 17:16 On Nov 11, 2011, at 10:01 AM, Andrew South wrote: Thanks Nate, hope it's a quick fix. Best wishes, Andy Hi Andy, All backlogged NGS jobs should now be running, new ones

Re: [galaxy-user] disk quota not updating

2011-12-05 Thread Nate Coraor
On Nov 30, 2011, at 12:49 PM, Richard Mark White wrote: Hi, I was nearing my disk quota (at 97%), so I deleted a large number of datasets using delete permanently. But my usage did not go down at all. Is there a delay in this happening, or is there some way to purge the files? Hi

Re: [galaxy-user] is public galaxy down?

2011-12-17 Thread Nate Coraor
On Dec 17, 2011, at 8:34 AM, Richard Mark White wrote: I am unable to access for past several hours. Are others having the same issue? Hi Rich, Our core router has crashed, we're working on the problem and hope to have it fixed within the next few hours. Sorry for the inconvenience.

Re: [galaxy-user] Finding Galaxy version

2011-12-19 Thread Nate Coraor
On Dec 13, 2011, at 5:33 AM, Paul-Michael Agapow wrote: A perhaps obvious question: how do I work out what version of Galaxy an instance is? This has come up a few times because of apparent bugs and different behaviour across various development and production instances. Now if you’re

Re: [galaxy-user] Tophat jobs not starting

2011-12-19 Thread Nate Coraor
On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote: Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have re-submitted everything again (2 jobs), but the same situation is happening. Is there

Re: [galaxy-user] Not able to get data from UCSC table browser

2012-01-03 Thread Nate Coraor
On Dec 22, 2011, at 5:35 PM, Sell, Christian wrote: Hi, I encountered similar problems today. I can’t open some histories, upload data or transfer data between histories. Regards Christian Hi, Due to extremely high load at the time, jobs were delayed. This has been resolved, so

Re: [galaxy-user] ftp upload

2012-01-03 Thread Nate Coraor
On Dec 27, 2011, at 8:52 PM, Gabor Bartha wrote: I have tried to use ftp to upload files to main.g2.bx.psu.edu but the jobs have been failing with: 421 service not available, remote server has closed connection after about 1.5GB. Isn’t ftp the way you are supposed to upload large files?

Re: [galaxy-user] Error during data upload of fastq.gz

2012-01-30 Thread Nate Coraor
On Jan 30, 2012, at 11:37 AM, Stefan Kroeger wrote: Hi Jen, On 30.01.2012 16:12, Jennifer Jackson wrote: Are you still having this problem? One thought is that this file is some sort of README file in with the other data files from you source. Another is that the data is an annotation

Re: [galaxy-user] ftp

2012-03-20 Thread Nate Coraor
On Mar 20, 2012, at 8:13 AM, Richard Mark White wrote: Hi, Is anyone else having trouble connecting to main.g2.bx.psu.edu for FTP uploads? I cannot seem to connect since yesterday. Hi Rich, It's back up now. --nate Rich ___

Re: [galaxy-user] Job is waiting to run

2012-03-22 Thread Nate Coraor
Hi Shisheng and Mónica, I see that jobs weren't dispatching on Galaxy Main, and have gotten them moving again. It'll take a bit to run through the backlog. Sorry for the inconvenience, and thanks for using Galaxy. --nate On Mar 22, 2012, at 5:30 AM, Mónica Pérez Alegre wrote: Hi Shisheng

Re: [galaxy-user] Problem using Galaxy

2012-05-23 Thread Nate Coraor
Hi, Please try starting with: $ LC_ALL=C ./run.sh --nate On May 18, 2012, at 11:22 AM, Seyed Mehdi Jazayeri wrote: Dear Sir/Madam, I am a PhD student working on RNA-Seq as my dissertation. As a matter of fact I want to do analyses of gene expressions for the sequences that I have

Re: [galaxy-user] FTP down?

2012-06-15 Thread Nate Coraor
On Jun 14, 2012, at 12:17 PM, John Clayton wrote: Dear Sir or Madam, I have been attempting to upload a few datasets (2Gb) for the past few days but I cannot seem to login to the server. This has been the case since the server crashed last week. Could you please restart the ftp server?

Re: [galaxy-user] Galaxy main not running jobs..

2012-06-18 Thread Nate Coraor
On Jun 16, 2012, at 7:38 PM, Jayaraman, Shyam wrote: Hi, My username is shyamsundar19...@gmail.com Galaxy main is not running jobs since today morning. They stay queued (gray) forever. I deleted and then re queued them twice. Still nothing.. Is the server down or is something wrong

Re: [galaxy-user] jobs not running on main server

2012-06-18 Thread Nate Coraor
On Jun 16, 2012, at 7:31 PM, Jacob Musser wrote: Hello, I uploaded a couple small files via ftp to do some basic text manipulation on them in the main galaxy server. I have queued up several jobs (including just importing the files I uploaded into a history) but after two hours of

Re: [galaxy-user] Include a data folder into Galaxy

2012-06-25 Thread Nate Coraor
On Jun 25, 2012, at 2:49 AM, Björn Grüning wrote: Hi Norbert, please have a look at the FTP-Upload feature from galaxy. The idea is that every user gets an FTP folder in which he can upload data. If you create such a directory you can probably link your data in such directories and galaxy

Re: [galaxy-user] Job is waiting to run for two days..

2012-06-25 Thread Nate Coraor
On Jun 25, 2012, at 1:53 PM, Shanshan Pang wrote: Hi, I am in the step map with bowtie with a status of JOB IS WAITING TO RUN for two days. I tried to re-run it, but did not work. So any suggestions on it? Thanks! Hi Shanshan, The cluster used to run mapping and other NGS tools is very

Re: [galaxy-user] file upload renamed

2012-08-22 Thread Nate Coraor
Hi Neil, You're looking for the option to link to data, which is explained here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files --nate On Aug 22, 2012, at 12:44 AM, neil.burd...@csiro.au wrote: When uploading a file using “Get Data” it seems the file is

Re: [galaxy-user] interupted running jobs restart

2012-09-11 Thread Nate Coraor
On Aug 27, 2012, at 8:53 AM, petr wrote: We are running galaxy on pbs cluster. In out setting some jobs can take several weeks to finish and it is virtually impossible to wait for suitable moment when server can be restarted or turn down without interrupting running tasks. Is there an option

Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions

2012-10-02 Thread Nate Coraor
On Oct 2, 2012, at 12:45 PM, greg wrote: Hi guys, I'm following the instructions here to install Galaxy on our SGE cluster. http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster (I'm aiming for the unified install) Here are a couple of questions I'm hoping someone could clear up for

Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions

2012-10-03 Thread Nate Coraor
On Oct 2, 2012, at 3:26 PM, greg wrote: On Tue, Oct 2, 2012 at 2:15 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Greg, You should start at the top level documentation for production servers: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server This includes

Re: [galaxy-user] Fastq-groomer help

2012-10-04 Thread Nate Coraor
On Oct 3, 2012, at 2:02 PM, Kshama Aswath wrote: Hello: I have this 20GB data that I have uploaded onto my history and trying to get it run thr groomer. Just the first data set was uploaded yesterday and ran groomer on it and it was not done this morning. The message indicated taht it is

Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server

2012-10-19 Thread Nate Coraor
On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote: Yes, daemon/stop-daemon is the best way. However, to stop a process that was not started with --daemon, this is what I do: ps aux | grep galaxy Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is

Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg

2012-11-05 Thread Nate Coraor
On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're

Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg

2012-11-05 Thread Nate Coraor
On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs

Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg

2012-11-05 Thread Nate Coraor
the top, where other variables are set. --nate Thanks again, Greg On Mon, Nov 5, 2012 at 3:33 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:26 PM, greg wrote: Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again

Re: [galaxy-user] [galaxy-dev] Account had be deleted ?

2012-11-09 Thread Nate Coraor
On Nov 7, 2012, at 5:47 AM, Diam Hsu wrote: Dear Sir or Madam, I used to use Galaxy to analyze NGS data, but these two days I could't login my Galaxy account, it also told me that my account has been marked deleted, and asked me to contact the Galaxy administrator to restore my

Re: [galaxy-user] Local Install - Understanding Upload File Concept

2012-11-16 Thread Nate Coraor
On Nov 16, 2012, at 10:41 AM, greg wrote: On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 9:14 AM, greg wrote: Are you running the upload tool on a cluster? --nate Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't verified

Re: [galaxy-user] Local Install - Understanding Upload File Concept

2012-11-16 Thread Nate Coraor
16, 2012 at 10:56 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 10:41 AM, greg wrote: On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 9:14 AM, greg wrote: Are you running the upload tool on a cluster? --nate Well I have Galaxy set

Re: [galaxy-user] Local Install - Understanding Upload File Concept

2012-11-16 Thread Nate Coraor
it? (Will it clean up anything placed in the new_file_path directory?) Thanks, Greg On Fri, Nov 16, 2012 at 10:56 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 10:41 AM, greg wrote: On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 9:14 AM, greg

Re: [galaxy-user] Problems with large gzipped fasta files

2013-02-13 Thread Nate Coraor
Hi Jim, Could you send me a URL to the dataset so I can grab a copy and try to reproduce this problem? Sorry for the trouble you've been having with the upload functionality and the delay in getting back to you. --nate On Feb 5, 2013, at 8:48 AM, Jim Robinson wrote: Hi, I am having a

Re: [galaxy-user] Problems with large gzipped fasta files

2013-02-13 Thread Nate Coraor
On Feb 13, 2013, at 12:25 PM, Jim Robinson wrote: Sorry Nate, I misunderstood at first, you want a URL to the dataset here on my server? I can definitely copy one up to an http server, I still have Ricardo's files on a hard disk. I'll start the copy now and let you know when its ready.

Re: [galaxy-user] Problem Loading History Pane

2013-02-15 Thread Nate Coraor
On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote: To whom it may concern: The History panel on the right side of the Galaxy page is taking a very very long time to load. Also, when it does load, I have tired to save my .bam files and the transmissions gets truncated to ~7000kb - 8000kb

Re: [galaxy-user] wrong disk usage figure reported on galaxy main

2013-03-07 Thread Nate Coraor
On Mar 7, 2013, at 4:46 AM, pbour...@agilent.com pbour...@agilent.com wrote: Hi, I noticed since yesterday that my “disk usage” % (top-right) has jumped from ~20% to ~ 80 % for no apparent reason. The added size of all my current histories is now only 29 Gb, which should be ~11%, and I

Re: [galaxy-user] problem with registration

2013-05-29 Thread Nate Coraor
On May 28, 2013, at 5:40 AM, Patel, Bella wrote: Hi I have tried to register for Galaxy but apparantly a user with my email address already exists! Very strange as I have never registered for this software. Can you advise? Bella Patel Hi Bella, It's possible that your account

Re: [galaxy-user] Galaxy server down?

2013-08-06 Thread Nate Coraor
Hi Sam, The job queue stalled over the weekend and has been recovering as of yesterday. All queued jobs should have run at this time, but if you are still experiencing problems, please let us know. Sorry for the inconvenience, and thanks for using Galaxy. --nate On Aug 5, 2013, at 7:53 AM,

Re: [galaxy-user] Egg build failed for numpy 1.6.0

2013-08-14 Thread Nate Coraor
Hi, Almost all of the Galaxy development team uses Macs, so it should certainly work. The problems with eggs, as you have both found, typically come with using non-standard versions of Python. Your best bet is to use the version that shipped with your version of OS X, which can be found in

Re: [galaxy-user] error message from Filezilla

2013-09-11 Thread Nate Coraor
On Sep 11, 2013, at 7:48 AM, Amit Pande wrote: Hi, I am getting the following error from the server : Command:USER genebus...@googlemail.com Response:331 Password required for genebus...@googlemail.com Command:PASS *** Response:530 Sorry, the maximum number of

Re: [galaxy-user] cannot download data to Galaxy

2013-09-11 Thread Nate Coraor
On Sep 11, 2013, at 9:56 AM, Elwood Linney wrote: Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like Sorry the maximum number of clients for this user

Re: [galaxy-user] Online galaxy turning everything red on RNAseq steps

2013-10-09 Thread Nate Coraor
The problem with cuffdiff should be fixed. Still looking at the tophat failures. Thanks for your patience, and for sticking with us as we iron this out. --nate On Oct 9, 2013, at 7:52 PM, Jennifer Jackson wrote: Hi Elwood, As I emailed to your direct question, we are looking at your bug

Re: [galaxy-user] can I use GlobusOnline to transfer data to the usegalaxy server instead of ftp

2013-10-16 Thread Nate Coraor
Hi Starr, Not currently, although we'll be looking in to setting up usegalaxy.org as a globus online endpoint in the near future. --nate On Oct 16, 2013, at 4:09 PM, Hazard, E. Starr wrote: Folks, Is it possible to use globusonline (https://www.globusonline.org) to move files to and

Re: [galaxy-user] Issues on RNAseq since the changeover

2013-10-18 Thread Nate Coraor
On Oct 18, 2013, at 12:48 PM, Elwood Linney wrote: My histories seem to be stopping their processing around the Tophat-cuffmerge steps since the change over of Galaxy online. Sometimes a red box appears over my history name but disappears in a minute or less. I am wondering, given the way

Re: [galaxy-user] problems in transitioning from Tophat to Cuffdiff

2013-10-22 Thread Nate Coraor
el linney On Tue, Oct 22, 2013 at 12:03 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Elwood, Jeremy and I took at a look at this. The failures in your history with this message: Error: number of labels must match number of conditions ...are due to a regression in the cuffdiff tool

Re: [galaxy-user] Pb with ftp connexion (FileZilla)

2013-11-08 Thread Nate Coraor
Hi Fabrice, Are you connecting to `usegalaxy.org`? This changed when we moved main.g2.bx.psu.edu to usegalaxy.org. Thanks, --nate On Nov 8, 2013, at 6:32 AM, Fabrice Besnard wrote: Hi, I am trying to connect to the Galaxy server via Filezilla in order to upload datasets. The connexion

Re: [galaxy-user] SNP finding

2013-11-11 Thread Nate Coraor
Hi Mark, This error is not tool related. Could you click the “bug” icon to send us an error report? —nate On Nov 11, 2013, at 8:33 AM, Mark Lindsay m.a.lind...@bath.ac.uk wrote: Dear Galaxy Users I wondered if anybody is having the same problem. I am trying to run CuffDiff using the

Re: [galaxy-user] jobs not running

2013-12-04 Thread Nate Coraor
Hi Ruth, The queue was very busy this morning as it would appear that someone is using the site for a workshop or class. I've cleared out these jobs since they were blocking regular use, and your jobs should begin running normally shortly. Sorry for the inconvenience. Thanks, --nate On Wed,

Re: [galaxy-user] Job of format conversion waiting for over 5 days

2014-03-31 Thread Nate Coraor
Hi Eduardo, I believe the job in question is not running because one of its inputs (#101) failed to have metadata set properly. This situation can be fixed by using the 'auto-detect' button on the failed dataset. --nate On Mon, Mar 31, 2014 at 5:20 PM, Eduardo Fox ofoxo...@gmail.com wrote: