On Jun 21, 2012, at 4:50 PM, Dorset, Daniel C wrote:
I have galaxy running on my institution’s cluster computing service, which
uses PBS. It’s in a balanced configuration.
Jobs going to the cluster submit without any problem at all. However, any job
that I have specified to run locally
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:
I have recently performed a fresh installation of Galaxy utilizing the latest
distribution and am getting a sizable number of errors when attempting to
start the server. The issue started when I performed a merge so I decided to
do the clean
On Jun 22, 2012, at 12:26 PM, Dorset, Daniel C wrote:
Good catch, thanks Nate! I have plenty of tool_runners defined, but no
tool_handlers. Do I have to specifically assign tool handlers in order for
them to be used in job deployment?
No, if you don't define any specific handlers in the
Hi Derrick,
If you use outputs_to_working_directory = True and put the working directory on
the SSD pool, writing during job execution will use the fast space. Once the
job completes, the outputs will be moved back to the larger, slower pool
configured for file_path.
--nate
On Jun 19, 2012,
On Jun 15, 2012, at 4:55 PM, Dellwo, Martin J. [JRDUS] wrote:
Hi there,
I am piloting my own instance of CloudMan in Amazon Web Services, using the
current public AMI (according to your Wiki), AMI: ami-da58aab3 and Name:
861460482541/galaxy-cloudman-2011-03-22.
I’d like to either
On Jun 18, 2012, at 5:04 AM, Ciara Ledero wrote:
Okay, so the only way for a user to upload a file with a size greater than
2GB is to use FTP? Or can a non-admin user be granted permission to upload
files using the filesystem path option, given that he/she can only access
his/her own
On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hello all,
I'm wondering if it is sensible to make Galaxy tools automatically use
the environment variable $NSLOTS to automatically adjust their
number of threads?
On Jun 15, 2012, at 11:27 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 4:06 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hello all,
I'm wondering if it is sensible
On Jun 10, 2012, at 10:36 PM, Ciara Ledero wrote:
Hi all,
I checked basics.py after reading a similar post and saw this:
self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None )
self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None )
Can you guys tell me what the
On Jun 11, 2012, at 3:45 PM, Fields, Christopher J wrote:
On Jun 11, 2012, at 9:10 AM, Nate Coraor wrote:
On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote:
Hi all,
So I was not able to configure Galaxy immediately after this post of mine
due to the tasks that I first needed to do
On May 31, 2012, at 11:19 PM, Ann Black-Ziegelbein wrote:
Hi -
I have been trying to run a quick test using the tool_dependency_dir
configuration option to prove out how it works ... but unfortunately I can't
get it to function right. I was hoping someone could point out my error. I
On Jun 1, 2012, at 5:31 AM, Sarah Maman wrote:
Hello Nate,
As agreed at the conference in Lyon, here's a screen printed my instance of
Galaxy (please look at the end of this mail), but the layout is not exactly
the same as that seen in the instance of Galaxy on the public server.
Hi
On Jun 4, 2012, at 7:24 AM, Peter Cock wrote:
Dear all,
Does Galaxy have any mechanisms to set the priority of jobs
submitted to the cluster? Specifically I am interested in SGE
via DRMAA, but this is a general issue. If there is some existing
code, I might be able to use it for the
On Jun 4, 2012, at 11:34 AM, Shantanu Pavgi wrote:
I am getting following errors in the galaxy log:
{{{
Error reading tool from path: human_genome_variation/sift.xml
Traceback (most recent call last):
File /home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py, line
315, in
Hi Jelle and Sarah,
I can't work on this issue right this moment, but have created an issue to
track so it's not forgotten:
https://bitbucket.org/galaxy/galaxy-central/issue/767/when-remote_user-true-a-lot-of-new-empty
--nate
On Jun 3, 2012, at 7:43 AM, Jelle Scholtalbers wrote:
Hi Sarah,
On Jun 5, 2012, at 6:08 PM, Dorset, Daniel C wrote:
I’m trying to troubleshoot why I can’t retrieve output from my Galaxy cluster
instance. I notice that when I click on any output, the URL is something like:
http://[root galaxy address]/datasets/[some 16-character hash]/display/[file
On Jun 1, 2012, at 4:36 AM, julie dubois wrote:
Hi,
After several post in an Apache Forum, I've solve any problem of my apache
configuration to enable load balancer configuration.
It seems work but when I launch my galaxy application, I arrive in this web
page :
Service temporarily
On May 22, 2012, at 11:18 AM, Peter Cock wrote:
On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl di...@immunbio.mpg.de wrote:
Thanks Peter! It's very likely that I have the exact same problem, because I
also have CentOS and needed to compile Python.
In that case make sure you've done this:
On May 19, 2012, at 10:09 AM, Peter van Heusden wrote:
Hi there
As I adapt Galaxy to the needs of the particular workflows I'm
implementing, I invariably end up tweaking the existing code,
especially the tool definitions and the datatypes config file. These
tweaks are often minor - e.g.
all
/Directory
--nate
On 16 May, 2012, at 3:57 AM, Nate Coraor wrote:
On Mar 14, 2012, at 9:16 PM, Huayan Gao wrote:
Yes, I did read the page and followed the instructions. But somehow, I keep
getting the error message, Forbidden……You don't have permission to access
/galaxy/static
On May 16, 2012, at 5:15 AM, julie dubois wrote:
Hi,
I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL
I've configured apache 2 with this lines on file
/etc/apache2/sites-available/default between VirtualHost and
/VirtualHost :
Proxy http://localhost:8080;
Order
On May 14, 2012, at 3:32 PM, Daniel Patrick Sullivan wrote:
Hi, Galaxy Developers,
I sent an email to this list earlier this week regarding an issue I
was having with the 'schedule jobs as user' functionality of Galaxy.
I am taking a closer look at the documentation on this configuration
On May 12, 2012, at 11:55 PM, Shantanu Pavgi wrote:
Hi,
At the risk of exposing of my Python ignorance, here is a doubt regarding
galaxy deployment. The galaxy application manages external dependency eggs
through it's custom ini specification file and eggs installation scripts. I
was
On May 16, 2012, at 2:57 PM, Anthonius deBoer wrote:
Hi,
In the latest Galaxy Central rev I get this error in each tool I run...
Any ideas what is going on?
Thanks,
Thon
WARNING:galaxy.datatypes.registry:Error loading datatype with extension
'wsf': 'module' object has no
On May 16, 2012, at 9:47 AM, Peter Cock wrote:
Hello all,
What is the current status in Galaxy for supporting compressed files?
Hi Peter,
Unfortunately, there's been nothing done on this so far. I'd love to see it
happen, but it hasn't been on the top of our priorities.
--nate
We've
On May 15, 2012, at 10:15 AM, Jean-Christophe Ducom wrote:
Thank you for your email Peter.
We have implemented Galaxy to interface with our HPC cluster via PBS/Torque.
Thanks to DRMAA (not PBS python) all user cpu usage can be accounted.The
motivation is indeed what you describe besides
~]$ sh galaxy-dist/run.sh
I could not figure it out what is wrong. Any suggestions?
Best,
Huayan
On 15 Mar, 2012, at 5:49 AM, Nate Coraor wrote:
On Mar 12, 2012, at 11:42 PM, Huayan Gao wrote:
Dear Nate,
I have a follow up question for you.
If I move galaxy out of my
On May 10, 2012, at 11:34 PM, Ciara Ledero wrote:
Hi all,
I would just like to ask if it's possible to create a new folder (via script)
in the galaxy-dist folder.
Hi Ciara,
If you mean a new Data Library folder, then yes, via the API. If you mean a
new subdirectory on the filesystem in
On May 10, 2012, at 4:23 PM, CHEBBI Mohamed Amine wrote:
Hi Galaxy team ;
I'am trying to put Galaxy into a production environment behind apache2 :
I followed the tuto in http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
for putting galaxy behind apache2 so I installed all the modules
] ) )
galaxy.eggs.EggNotFetchable: ['Cheetah']
That's pretty odd, you're executing this on the Galaxy server? What happens if
you run fetch_eggs.py in the same directory?
--nate
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Friday, May 11, 2012 3:54 PM
To: Kelkar
On May 11, 2012, at 4:18 PM, Kelkar, Hemant wrote:
No I did not execute it on the galaxy server. I do not have shell access to
the blade that actually runs the galaxy server.
So I would need to get my sys admin to run this then?
Not necessarily, as long as you are running it as the same
On May 9, 2012, at 10:37 AM, Tilahun Abebe wrote:
Hi Jen,
Thank you for the suggestions. I did try to log in to Galaxy under User
--Login. The password is the one I use for the Galaxy Main. However, it
gives me the error message No such user (please note that login is case
sensitive). I
On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote:
I have had Galaxy running on a local BAS, and after success with that we’re
ready to create an instance on our local cluster computing service. The local
cluster uses PBS/Torque.
I’m familiar with the basics of configuration, but our
On May 3, 2012, at 5:24 AM, Frank Sørensen wrote:
Hi Guys,
After the most recent 'hg pull -u' followed by 'hg merge', I get the
following error in paster.log when I try to restart Galaxy:
galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,375 Loaded history export
tool: __EXPORT_HISTORY__
Hi Graham,
Thanks for the heads up. It's been fixed.
--nate
On May 2, 2012, at 9:39 AM, graham etherington (TSL) wrote:
Hi,
The Galaxy Toolshed is giving a 502 Bad Gateway error. Is there a problem
with it at the moment?
If so, is it just a matter of restarting it or is there a likelihood
that is.
--nate
Thanks,
Liram
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Monday, April 30, 2012 11:29 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: galaxy-...@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1)
Subject: Re: [galaxy-dev] Remove libraries using Galaxy code or API
On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote:
This is my code for running a samtools command internally, via Galaxy:
open INP, $ARGV[0]
or die Cannot open file: $!;
$file = $ARGV[1];
open OUT, $file
or die Cannot open file: $!;
@out =
On Apr 29, 2012, at 9:26 PM, Ciara Ledero wrote:
Hi all,
Can I ask what this line of code does?
job_wrapper.finish( stdout, stderr )
It's the one from the local.py.
Hi Ciara,
This runs the JobWrapper.finish() method in
galaxy-dist/lib/galaxy/jobs/__init__.py, which performs all the
On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote:
This is my code for running a samtools command internally, via Galaxy:
open INP, $ARGV[0]
or die Cannot open file: $!;
$file = $ARGV[1];
open OUT, $file
or die Cannot open file: $!;
@out =
On Apr 26, 2012, at 11:03 AM, Hans-Rudolf Hotz wrote:
On 04/26/2012 04:47 PM, Peter Cock wrote:
On Fri, Mar 16, 2012 at 11:00 AM, Peter Cockp.j.a.c...@googlemail.com
wrote:
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraorn...@bx.psu.edu wrote:
On Feb 10, 2012, at 6:47 AM, Peter Cock
On Apr 25, 2012, at 9:22 AM, Louise-Amélie Schmitt wrote:
Hi everyone,
I'm (still) having issues with running jobs as the real user on our PBS Pro
cluster. When I try running a job, it ends up in error state and displays
the following error message:
tou!
ch: cannot
touch
On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote:
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the galaxy
user. Any clue?
Hi L-A,
There are actually two dataset attributes for
On Apr 25, 2012, at 8:25 AM, Louise-Amélie Schmitt wrote:
Hi,
Thanks a lot it actually helped. It is not exactly as straightforward in
drmaa.py but somehow I could manage.
However, it was not the problem. For some reason, the user needs to write
files from the node to
On Apr 24, 2012, at 8:36 PM, Michael Moore wrote:
There is apparently a persistent problem with samtools which normally lives
at /usr/bin/samtools. I encountered a similar problem in Python when
uploading BAM files.
I did not resolve the problem. I hacked for a while on binary.py in a
On Apr 23, 2012, at 10:31 PM, Ciara Ledero wrote:
Hi all,
According to Galaxy, uploading files larger than 2GB will surely fail. For
this reason, uploading via FTP is recommended. Unfortunately, I cannot
download/install an FTP server for Galaxy since I am working on a remote
server. I
Hi Kiran,
This is a question best directed to the galaxy-dev list, which I have CC'd.
On Apr 23, 2012, at 5:23 AM, Kiran Jaycee wrote:
Dear Nate,
Im deploying Galaxy in the cluster environment with 8 nodes and 96 cores. Im
particularly interested in running NGS tools
like BWA, BOWTIE etc
On Apr 23, 2012, at 4:55 AM, liram_va...@agilent.com
liram_va...@agilent.com wrote:
Hello,
I am using Galaxy API for some actions and I must say that this is indeed a
really great feature with a great power.
Anyway, I am trying to write a python script that one of its goals is to
Hi Ryan,
I like that it's user-directed, and we could be there to provide input,
although if help is needed to organize the call we could probably assist with
that. I plan to be on the call as often as my schedule allows, and I believe
some of the other developers on the team would also be
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:
Hello,
After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run
properly (output files OK) but I get the following warning:
/WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be
fetched/
Hi
On Apr 19, 2012, at 11:12 AM, Nate Coraor wrote:
On Apr 19, 2012, at 10:44 AM, Peter Cock wrote:
On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor n...@bx.psu.edu wrote:
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running
galaxy-dist when using the task splitting functionality? I'm using the
latest code from the default branch, changeset: 7027:f6e790d94282
Hi Peter,
This was resolved in
On Apr 19, 2012, at 10:44 AM, Peter Cock wrote:
On Thu, Apr 19, 2012 at 2:53 PM, Nate Coraor n...@bx.psu.edu wrote:
On Apr 17, 2012, at 9:04 AM, Peter Cock wrote:
Hi all,
Does anyone know what might have introduced this problem running
galaxy-dist when using the task splitting
On Apr 16, 2012, at 9:03 PM, Jose Navas wrote:
Hi everybody,
I was searching through the Galaxy code and I find the solution: the function
responsible for copying files is using shutil.copy function, which only
allows copy files. I've modified this function to use shutil.copytree in case
On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote:
Dear all,
I was trying to run the build-in function Fetch taxonomic representation
on my local instance of Galaxy, however it doesn't work as I expect.
The error message is:
/bin/sh: taxBuilder: not found
Anyone has seen this problem
Thanks for the example, Frank.
You can upload to data libraries directly from the local filesystem. The
relevant documentation is here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Eli, with respect to the question about modifying galaxy-dist/lib:
On Apr 16, 2012, at 7:13 AM, Eli Reuveni wrote:
Hi,
I am getting the error “This link may not be followed from within Galaxy.”
When I try to upload a data file to my local galaxy.
I have traced back the error to root.py (RootController class).
Could anyone help me with that?
Hi
On Apr 9, 2012, at 3:04 AM, Praveen Raj Somarajan wrote:
Hello,
Just want to clarify two questions:
1) Is there a way to get the absolute path of a dataset directly from the
interface? This is sometimes useful to create a local directory of all
required files (by using symlink) if we
On Apr 6, 2012, at 2:31 PM, Robert Chase wrote:
Hello,
On our test instance of galaxy we have set up filesharing with the rest of
our cluster. We have also setup LDAP authentication on the server.
We are having problems getting data from the tools based on data_source.py.
For instance,
On Mar 30, 2012, at 5:53 AM, Alban Lermine wrote:
Hi,
It seems that PYTHONPATH isn't set when galaxy start.. (according to
http://osdir.com/ml/galaxy-development-source-control/2011-11/msg00035.html)
Should I search this way ?
Hi Alban,
Galaxy should be setting PYTHONPATH itself, it's
On Mar 9, 2012, at 4:12 AM, Yuri D'Elia wrote:
Hi everyone. I've set up a galaxy production environment and it seems to be
working.
I've identified a couple of issues though:
If I enable apache_xsendfile, the little eye icon (Display data in
browser) on each dataset stops working. I get
On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote:
Hi,
I would like to know which tool_conf.xml to use, and would like to know the
difference between the main and the sample one. I know that the functional
tests are running against the tool_conf.xml.sample but what
tool_conf.xml.main is
Hi Anne,
We're aware that many tests require certain local data to be set up beforehand.
As such, these tests can't really be run at a local site. As part of
relocating our tools to the tool shed, we hope to fix this issue.
Thanks,
--nate
On Feb 20, 2012, at 1:25 PM, Anne Pajon wrote:
From: Nate Coraor n...@bx.psu.edu
To: Liisa Koski liisa.ko...@dnalandmarks.ca
Cc: galaxy-dev@lists.bx.psu.edu
Date: 01/30/2012 03:07 PM
Subject: Re: [galaxy-dev] Error Setting BAM Metadata
On Jan 25, 2012, at 2:43 PM, Liisa Koski wrote:
Hello,
I am trying to upload BAM
On Feb 7, 2012, at 5:52 AM, Federico De Masi wrote:
Dear colleagues,
I have been struggling with this issue for quite a while now, and I don't
seem to find a solution (neither in situ nor in webo).
here it is:
Because of the confidentiality of our data, I have setup both a Galaxy
On Mar 10, 2012, at 6:25 PM, Luciano Cosme wrote:
Hi,
I uploaded 11 files today (1 to 2Gb compressed files) to my local instance
without a problem (as admin). Then I got this error message below and it get
stuck at This dataset is uploading and I could not upload the last files.
Is
On Mar 12, 2012, at 5:15 PM, jiechenable1...@gmail.com wrote:
Dear Nate,
Sorry to trouble you. I know that you are busy, but this problem has annoyed
me for couple days. Please help.
I want to enable uploading via ftp for my local Galaxy instance. I followed
the instructions under the
/Apache%20Proxy
--nate
Best,
Huayan
On 14 Feb, 2012, at 1:21 AM, Nate Coraor wrote:
On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote:
Hi Nate.
I am ok now.
The code I copied from wiki was using galaxy_dist, while my folder name is
galaxy-dist.
After I changed the path
On Mar 12, 2012, at 2:23 PM, Fields, Christopher J wrote:
You can change the default location of tmp files by modifying the
environment; we ran into this with samtools directly dumping temp sort files
to a local node, causing the job to shut down. Setting TMPDIR worked for me.
Hi Chris,
On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote:
Hi Alban,
Is your Galaxy server behind a firewall or without network access such that
it cannot access http://eggs.g2.bx.psu.edu/ ?
What happens if you run `python scripts/fetch_eggs.py` by hand?
Is there a way to downgrade Galaxy?
On Mar 13, 2012, at 6:59 AM, David Matthews wrote:
Hi,
We emailed previously about possible memory leaks in our installation of
Galaxy here on the HPC at Bristol. We can run Galaxy just fine on our login
node but when we integrate into the cluster using pbs job runner the whole
thing
On Mar 13, 2012, at 10:36 AM, Alban Lermine wrote:
Hi,
I run upgrade: hg pull -u -r 40f1816d6857 on our local instance, and I'm
now unable to start Galaxy..
Here is the content of Galaxy_log:
Traceback (most recent call last):
File galaxy_dir/galaxy-dist/lib/galaxy/web/buildapp.py,
On Feb 29, 2012, at 11:34 AM, Jorrit Boekel wrote:
Dear list,
Our lab's proteomics data is frequently outputted into 50 files containing
different fractions of proteins. The files are locally stored and not present
on the Galaxy server. We've planned to somehow (inside galaxy) merge these
There is also a memory leak that occurs when using the pbs job runner. I
believe the leak is somewhere in libtorque or pbs_python but I have not yet
tracked it down.
--nate
On Feb 29, 2012, at 3:28 PM, John Chilton wrote:
We had intermittent issues like this for an embarrassingly long time
On Feb 29, 2012, at 11:50 AM, Michael Burrell (TOC) wrote:
Good evening all,
I am seeing the following issue when attempting to start galaxy.
Traceback (most recent call last):
File ./scripts/paster.py, line 34, in module
command.run()
File
On Mar 1, 2012, at 8:49 AM, Waldron, Michael H wrote:
I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12.
I am trying to enable use of Mpileup for SAM Tools, and have added the entry
for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup
Galaxy, the
On Feb 14, 2012, at 11:07 PM, Jose William Valero Velasquez wrote:
Hi,
I'm writing you because i'm trying to install galaxy in a server running suse
behind a proxy, so i have to build the eggs like if the server were offline,
in the guide says that i should execute the command
By any chance, do you all happen to be using the nginx upload module? I am
guessing not.
--nate
On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote:
I confirm the same strange behaviour since some of the last updates on the
central version. We are at the latest now.
It is also with medium
, Nate Coraor wrote:
On Jan 18, 2012, at 11:54 AM, Ryan Golhar wrote:
Nate - Is there a specific place in the Galaxy code that forks the
samtools index on bam files on the cluster or the head node? I really
need to track this down.
Hey Ryan,
Sorry it's taken so long, I've been pretty
...@uab.edu wrote:
Just wanted to add that we have consistently seen this issue of 'samtools
index' running locally on our install. We are using SGE scheduler. Thanks for
pointing out details in the code Nate.
--
Shantanu.
On Jan 20, 2012, at 9:35 AM, Nate Coraor wrote:
On Jan 18
uploading at some point.
--nate
On 31/01/2012, at 7:12 AM, Nate Coraor wrote:
On Jan 26, 2012, at 4:29 AM, Hans-Rudolf Hotz wrote:
On 01/25/2012 08:20 PM, Kim, Hyunsoo wrote:
Hi again,
I'm kind of lost here. Does Data Library allow regular users to upload
files directly
On Feb 10, 2012, at 6:47 AM, Peter Cock wrote:
Hello all,
I've noticed we have about a dozen stalled upload jobs on our server
from several users. e.g.
Job IDUserLast Update ToolState Command LineJob
Runner PID/Cluster ID
2352 21 hours ago
On Feb 10, 2012, at 7:06 AM, Peter Cock wrote:
Hi all,
I've just updated our Galaxy to the current release 26920e20157f which
now includes quota support. This means I need to run
set_dataset_sizes.py in order to record the current usage, as
explained here:
, http://61.244. xxx.xxx.
Then how should I set up in httpd.conf file so I can access galaxy using my
ip address, for example, http://61.244. xxx.xxx/galaxy?
Thanks,
Best,
Huayan
On 10 Feb, 2012, at 1:17 AM, Nate Coraor wrote:
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote
On Feb 13, 2012, at 7:38 AM, Sarah Maman wrote:
Hello,
I managed to connect to Galaxy to LDAP ;-)
Three points were blocking for me:
* Being root of my virtual machine can carry out tests
* I confused login / password of two LDAP, so I thought that my
authentication method was not good
On Feb 13, 2012, at 11:07 AM, p.baska...@leeds.ac.uk wrote:
Hi Nate,
I got the following error in the log file after running cufflinks on the
local instance of galaxy:
Hi Praveen,
Please use the galaxy-dev mailing list (CC'd) for these types of questions so
that you can receive a more
On Feb 13, 2012, at 11:52 AM, Fields, Christopher J wrote:
On Feb 13, 2012, at 9:45 AM, Nate Coraor wrote:
On Feb 8, 2012, at 9:32 PM, Fields, Christopher J wrote:
'samtools sort' seems to be running on our server end as well (not on the
cluster). I may look into it a bit more myself
On Feb 8, 2012, at 1:00 AM, Huayan Gao wrote:
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror
site. The mirror site works well. I installed the galaxy in the same server.
Now my question is: how to set up httpd.conf file so I can access both
Hi Charlie,
Just a minor correction, the Main server is Solaris 10, the clusters on which
jobs run are Debian testing/unstable and RHEL 5.7.
--nate
On Feb 6, 2012, at 9:01 PM, Dannon Baker wrote:
Hi Charlie,
Our main galaxy server is actually running CentOS 5.10. The galaxy cloud
On Feb 6, 2012, at 1:27 PM, Zachary Charlop-Powers wrote:
Hi Galaxy Team,
I am running a small local instance of Galaxy and I've run into a database
error following an upgrade to the Jan27th galaxy-dist release.
The last line when I run run.sh tells me to upgrade my database:
.
--nate
From: Nate Coraor n...@bx.psu.edu
To: Rehan Saleem pk_re...@yahoo.com
Cc: galaxy-dev@lists.bx.psu.edu galaxy-...@bx.psu.edu
Sent: Monday, February 6, 2012 10:19 PM
Subject: Re: [galaxy-dev] Postgresql To Galaxy
On Feb 6, 2012, at 10:56 AM, Rehan Saleem wrote:
Hi Nate,
well
On Feb 6, 2012, at 6:37 AM, Rehan Saleem wrote:
Hi ,
i have created postgreSQL database where i have created all functions and
views which performs annotations and some other functions , how can i show my
postgresql database table to galaxyas output . i have connected my database
from
On Feb 4, 2012, at 7:53 AM, Matloob Khushi wrote:
Hi Galaxy Developers
I aim to write a tool that will interact with Postgres database; here is what
I wrote to test database connectivity. This script resides in
/galaxy-dist/tools/test_tool/ and gets invoked from the front end. However
the tool has some means of knowing what host, user and port to connect
to, and the setup of this information is the same as it would be when running
it on the command line (via a config file, environment, hardcoded in the
tool...?).
--nate
From: Nate Coraor n...@bx.psu.edu
To: Rehan Saleem
On Feb 3, 2012, at 7:30 AM, Peter Cock wrote:
On Fri, Feb 3, 2012 at 11:55 AM, Ryan Golhar
ngsbioinformat...@gmail.com wrote:
'qstat -f | grep jobname' will give you the full jobname without truncation.
Sadly not on our version of SGE - which appears to be SGE 6.2u5 - you
get a bit more
On Feb 6, 2012, at 1:05 PM, Nate Coraor wrote:
On Feb 3, 2012, at 7:30 AM, Peter Cock wrote:
On Fri, Feb 3, 2012 at 11:55 AM, Ryan Golhar
ngsbioinformat...@gmail.com wrote:
'qstat -f | grep jobname' will give you the full jobname without truncation.
Sadly not on our version of SGE
with:
% python -ES ./scripts/fetch_eggs.py
If this works and running Galaxy still fails, you may need to set up a
virtualenv as described here:
http://usegalaxy.org/production
Sorry for the inconvenience.
--nate
Thanks again!
Lu
On 1/30/12 20:37 , Nate Coraor wrote:
On Jan 30, 2012
On Feb 2, 2012, at 10:35 AM, Shantanu Pavgi wrote:
Peter,
I am having similar issue and it started happening only after the recent
update. See:
http://galaxy-development-list-archive.2308389.n4.nabble.com/job-cleanup-files-drmout-and-drmerr-not-found-td4341867.html
I haven't had
On Feb 2, 2012, at 12:22 PM, Nate Coraor wrote:
On Feb 2, 2012, at 10:35 AM, Shantanu Pavgi wrote:
Peter,
I am having similar issue and it started happening only after the recent
update. See:
http://galaxy-development-list-archive.2308389.n4.nabble.com/job-cleanup-files-drmout
On Feb 2, 2012, at 12:23 PM, Shantanu Pavgi wrote:
The job scripts generated by galaxy contain following code. I was wondering
what's the purpose of if-block after setting 'GALAXY_LIB=None' assignment.
{{{
GALAXY_LIB=None
if [ $GALAXY_LIB != None ]; then
if [ -n $PYTHONPATH ]; then
Alex
Am 12.12.2011 um 16:11 schrieb Nate Coraor:
On Dec 9, 2011, at 6:45 AM, Alexander Graf wrote:
Hello,
I have recently updated our Galaxy dist and I'm running into problems
viewing BAM files in IGV (v2.0.22), saying: Invalid GZIP header.
Hi Alex,
Your config below looks
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