On Nov 8, 2011, at 10:42 PM, Greg Von Kuster wrote:
James,
In addition to Ross's comments, consider that the base class of all Galaxy
datasets ( library datasets, etc ) is the DatasetInstance class, whose
get_file_name() method leverages the file_name property from the Dataset
class (
On Oct 5, 2011, at 10:01 AM, Nikolai Vazov wrote:
Hi,
I can't find out how to use the dropdown User type which is displayed after
I select User Register in the start page of Galaxy. Do I have to define the
types myself? Are they pre-set? The dropdown menu just says Select one, but
the
just
changed shutil.mv to os.system(mv) because it has less baggage. In fact if I
comment it out the upload still works.
Ilya
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Monday, November 07, 2011 7:57 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, November 04, 2011 4:50 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Looks like actual user breaks splitting
I am getting
On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote:
Hi,
Reading a little more about this problem, I see Galaxy uses python
tempfile library (http://docs.python.org/library/tempfile.html),
specifically at line 70 in tools/samtools/sam_to_bam.py:
tmp_dir = tempfile.mkdtemp()
mkdtemp should
On Sep 29, 2011, at 11:02 PM, KOH Jia Yu Jayce wrote:
Hi
I’d like to enquire about the bug report. Apparently when someone sends a bug
report, everyone in the mailing list and the sender himself are supposed to
receive the bug report (as can be seen in the to field in the email sent
On Sep 30, 2011, at 9:32 AM, Iry Witham wrote:
When I run sh manage_db.sh upgrade I get the following error:
Hi Iry,
Sorry for missing this - were you ever able to resolve it?
Thanks,
--nate
2 - 3...
Traceback (most recent call last):
File ./scripts/manage_db.py, line 55, in module
On Oct 21, 2011, at 7:55 PM, Robert Day wrote:
Hi,
Sorry to bother you guys with such a simple thing. I'm quite new to the
terminal and command line etc. so downloading and getting Galaxy running on
my PC was a voyage of discovery! Anyhow, I have it, it's alive.. just
can't get
On Nov 2, 2011, at 4:48 PM, Arthur Goldberg wrote:
Hi
Where's the best documentation for parallel cluster support in Galaxy, please?
Hi Arthur,
Our documentation on running Galaxy as a production service, including on a
cluster, is available here:
http://usegalaxy.org/production
If
On Nov 2, 2011, at 4:45 PM, Oren Livne wrote:
Dear Nate,
My PYTHONPATH is already set to this value.
Hi Oren,
Is it exported? If it's set to Galaxy's lib directory, it should not be
possible that the galaxy module can't be found.
--nate
Best,
Oren
On Oct 27, 2011, at 8:23 AM, SHAUN WEBB wrote:
Hi, I updated my test server today and everything seemed fine. I added a new
library item via a URL. After that my history panel displays Internal Server
Error and I am getting the error below in paster.log:
Any ideas how this has occurred
On Oct 24, 2011, at 9:01 AM, Martin Dahlö wrote:
Hello there
As the subject hints, I am trying to export histories through the API.
Doing it through the web interface is a breeze, but has it been
implemented in the API yet? I could not find anything about it in the
examples or by searching
On Oct 25, 2011, at 2:43 AM, Andrew Warren wrote:
Hello,
I recently encountered a problem when trying to run Cufflinks on eight BAM
files on our galaxy instance (via the multi-input toggle) and received the
error: Unable to run job due to a misconfiguration of the Galaxy job running
Shantanu Pavgi wrote:
On Nov 2, 2011, at 3:39 PM, Nate Coraor wrote:
Shantanu Pavgi wrote:
Hi,
It seems like modification of 'citation_url' in the universe_wsgi.ini
config file has no effect in the UI (Help -- How to Cite Galaxy). Is it
something hard-coded in the source
Nate Coraor (n...@bx.psu.edu) wrote:
Duddy, John wrote:
I'm not following you - it's been 6 months since I wrote that code ;-}
I know the feeling!
IT looks to me like a DatasetPath() object is always placed in that array,
and with one exception near then, it looks like the change I
...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Monday, October 31, 2011 8:37 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Re Acutal user code
It seems to be working but when I run BWA or Bowtie it finishes green but the
files are empty. Doesn't give
results by EOD.
Yeah, there is probably a problem with splitting, I was about to test
that myself.
Ilya
-Original Message-
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
Sent: Wednesday, November 02, 2011 9:15 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Cinto Queky wrote:
Hi All,
We encountered queuepool limit problem after running the workflows for a few
times.
We have tried to increase these 2 parameters:
database_engine_option_pool_size and database_engine_option_max_overflow to
20 and 40 respectively.
Are there other parameters
Shantanu Pavgi wrote:
Hi,
It seems like modification of 'citation_url' in the universe_wsgi.ini config
file has no effect in the UI (Help -- How to Cite Galaxy). Is it something
hard-coded in the source?
Hi Shantanu,
Whoops. This has been fixed in 6205:9a9479f7e53f.
--nate
--
Oren Livne wrote:
Dear All,
I am running the example_watcher_folder.py API script and it
intermittently fails to run a workflow on a file dropped into the
import directory (the file is imported and the workflow starts
running, but its jobs hang or fail). Galaxy uses a condor dramaa job
Jerico Nico De Leon Revote wrote:
Hi,
I'm just doing a simple get-data from UCSC on our local Galaxy
instance and got the following error:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
The job box then is displayed as red on the history panel.
The
Hans-Rudolf Hotz wrote:
Hi Andrew
you might wanna look at the Config files listed in the '.hgignore' file.
I usually do a quick diff on the new *.sample file with a copy of
the previous file and then merge any required changes into the
actual file.
This is essentially what I do when I
Brad Langhorst wrote:
On 10/19/11 3:09 AM, Amit Anand a...@tll.org.sg wrote:
Hi,
I have just installed a local instance of galaxy. Though I am not too
familiar
with unix, I preferred a local instance because of large amount of data I
have
to process. However, I am unable to
Li, Jilong (MU-Student) wrote:
Hi,
When I installed galaxy, one error message appeared, which said that
ImportError: No module named distutils.util
Fetch failed.
Could you tell me how to solve this problem?
Thank you very much!
Hi Jilong,
Since this is a question regarding a local
for galaxy - ucsc page return when
the url is :8080/galaxy and not just /galaxy?
Not off the top of my head. I have this message marked, I'll take a
look as soon as I have time.
--nate
thanks,
joe
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday
Stephen Eacker wrote:
Hello,
I'm trying to upload a 600MB BAM file to my local instance of Galaxy
but the upload fails. I tried to follow a thread on this topic archived on
osdir.com but could not find if the issue was resolved. My BAM file has been
previously been sorted and
Joseph Hargitai wrote:
Hi,
i was browsing through the list and found many entries for this issue but not
a definite answer.
We are actually running into this error for simple file uploads from the
internal filesystem.
Hi Joe,
This error occurs when the job's standard output and
Chorny, Ilya wrote:
Nate,
I have been trying to figure out how to make the changes you suggested (i.e.
write output files to the job_working_directory) and then move them over to
files but I am having a difficult time navigating the code. If you could
point me in the right direction,
SHAUN WEBB wrote:
Hi Nate.
Could you provide more info on how to run this script. I have a
history and dataset name and I want to find the file stored on the
server.
Hi Shaun,
You'll need the dataset ID, which you can see as part of the URL of many
of the links in the history item. For
Lukasse, Pieter wrote:
Hi Peter,
Thanks for the reply.
Does anyone know how to execute a specific workflow from the command prompt?
E.g. run the workflow as a job? Then I could perhaps write a workflow wrapper
tool to overcome this shortcoming.
Hi Pieter,
Have a look at
Hey Ilya,
I'm looking at it now, I'll let you know asap (should be tomorrow).
--nate
Chorny, Ilya wrote:
Nate,
I have been trying to figure out how to make the changes you suggested (i.e.
write output files to the job_working_directory) and then move them over to
files but I am having a
lenta...@jimmy.harvard.edu wrote:
Hi,
I noticed on that on the manage users page, even after deleting and
purging users (by clicking on the delete and purge buttons on that page),
their account still sticks around in the db. How does one remove these
accounts permanently? Is there a
Dannon Baker wrote:
Oren,
I've moved this thread over to the galaxy-dev mailing list since it deals
with a local installation. Users on this list are more likely to have an
answer for this type of question.
That said, we don't officially support running Galaxy under Cygwin (or
Oren Livne wrote:
Dear Nate,
I've been doing exactly that. What's driving me crazy is that every
second compile (bx_python, numpy, pysam) runs into a Cygwin DLL
remap failure that cannot be resolved with /bin/rebaseall. So any
advice on how to get rid of that would be great. Right now it's
Lance Parsons wrote:
I'm running a local instance of Galaxy that has been working quite
well. However, I've recently run into a problem when importing
datasets from a data library into a history. The Size on Disk of
the history grows by the size of the imported dataset, however, the
new
Bossers, Alex wrote:
Since some time we are observing strange things happening to using files from
our local data libraries in our local galaxy-central instance:
The files and hierarchy stay there but when copied to the history. they
turn up as being deleted and can only be used by
Jean-Baptiste Denis wrote:
Hello evyerbody,
i guess this question has already been answered, but i didn't find any :/
Is there a way to reload a tool file from the command line ? I'd
like to automate the process when a user upload a new version of an
existing tool. Am I reinventing the
in your environment as
it is in his).
If no answers turn up in a few days, then we can open an issue for it in
Bitbucket.
--nate
Lance
Nate Coraor wrote:
Lance Parsons wrote:
I'm running a local instance of Galaxy that has been working quite
well. However, I've recently run into a problem
Nate Coraor wrote:
michael burrell (TOC) wrote:
Good afternoon all,
I am having some issues with hg performing an update, it wants to use
vimdiff and this is not the way I like to work. According to the mercurial
simply placing the folloing in the ~/.hgrc should make mercurial
: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, September 30, 2011 11:03 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
Paniagua, Eric wrote:
Hi Nate,
Thank you for your response! I am glad that it was you
Mike Wallis wrote:
Hello,
I'm trying to get an instance of Galaxy working where the application server
- the web front end, as I understand it - is on a completely separate host to
the SGE cluster the back end runs on. Is there any way of setting up galaxy
that it uses ssh instead of
.
--nate
Thanks again,
Ann
On Sep 28, 2011, at 9:29 AM, Nate Coraor wrote:
Ann Black wrote:
Hello -
I am working on standing up our own galaxy installation. We would like to
have galaxy front multiple clusters, and I have some questions I was
hoping someone could help
,
Could you put these patches in an issue (or create a pull request)?
Thanks,
--nate
Lance
Glen Beane wrote:
On Sep 27, 2011, at 1:14 PM, Nate Coraor wrote:
Glen Beane wrote:
We recently updated to the latest galaxy-dist, and learned that the
sam_merge.xml tool now uses picard
Bruno Zeitouni wrote:
Dear all,
I would like to use our built-in color-spaces indexes for BWA with
Galaxy but I failed to do it.
I added the following line in the bwa_index_color.loc file of the
tool-data directory :
hg19 hg19 hg19 my_path_to/hg19.fa
but I don't see
James Vincent wrote:
Hello,
I've read about a number of side projects that integrate iRODS or
other file handling things into Galaxy.
What are the chances Galaxy could be made to use iRODS as it's primary
file store? Instead of storing all files in some local space on a
machine, Galaxy
Haden, Kirt wrote:
Hi,
When I run Galaxy under Python 2.7, I am unable to run SAM to BAM tools
without getting the following error (below). The same configuration with
Python 2.6 does not have an issue. The error seems to indicate bx_python eggs
are not fetchable. What am I doing
?
From: Nate Coraor [n...@bx.psu.edu]
Sent: Wednesday, September 28, 2011 9:24 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
Paniagua, Eric wrote:
Hi all,
Can anyone tell me why
.
--nate
Chorny, Ilya wrote:
Same permissions as the 2.6 egg.
-Original Message-
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Friday, September 30, 2011 8:59 AM
To: Chorny, Ilya
Cc: Nate Coraor; Haden, Kirt; 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev
Hi Matloob,
It looks like urllib, which Galaxy uses to fetch eggs, can't use
authenticated proxies. urllib2 would do it:
http://stackoverflow.com/questions/34079/how-to-specify-an-authenticated-proxy-for-a-python-http-connection
But this would require some changes to the egg handling
Paniagua, Eric wrote:
Hi all,
Can anyone tell me why JobWrapper.finish() moves the primary dataset file
dataset_path.false_path to dataset_path.real_path (contingent on
config.outputs_to_working_directory == True) but does not move the extra
files? (lib/galaxy/jobs/__init__.py:540-553)
Paniagua, Eric wrote:
Hi everyone,
I am experiencing a similar problem to that of Leandro. I have defined a new
datatype deriving Data, and having extension foobar. The simplest and
first thing I'd like to do with it is create a dataset of this new type
Foobar by uploading from my
Colleen Doherty wrote:
Hi,
I get the following error when trying to upload data to Galaxy
AttributeError: 'NoneType' object has no attribute 'lower'
Same error for many different types of files (fastq, sam, bam) some of
which uploaded last week.
What I've tried:
Deleting browser cache
Simon Taylor wrote:
Hi,
What exactly are the two options database_engine_option_pool_size and
database_engine_option_max_overflow in universe_wsgi.ini?
Hi Simon,
These are explained in the SQLAlchemy documentation:
http://www.sqlalchemy.org/docs/05/reference/sqlalchemy/pooling.html
Timothy Wu wrote:
On Thu, Sep 15, 2011 at 5:32 PM, Timothy Wu 2hug...@gmail.com wrote:
On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock
p.j.a.c...@googlemail.comwrote:
On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu 2hug...@gmail.com wrote:
I think I need some kind of data source
mallika V wrote:
hi
I am very new to the galaxy software. I have to convert one fastq file of
nearly 5 gb size and unable to do that. i tried to install galaxy in locally
but it tells some eggs are out of date. Can anyone plz help me in this
regard
Hi,
With respect to the public version of
Glen Beane wrote:
We recently updated to the latest galaxy-dist, and learned that the
sam_merge.xml tool now uses picard MergeSamFiles.jar to merge the files
instead of the samtools merge wrapper sam_merge.py.
this is a problem for us because MergeSamFiles.jar does not honor $TMPDIR
when
Hi Alex,
That code is ancient - I would suggest disabling the memdump in your
configuration unless you need it.
--nate
Alex R Bigelow wrote:
Hi,
I restarted my Galaxy server this morning (it was working fine before), but
now I'm getting the following error:
Error at initialization of
Glen Beane wrote:
On Sep 13, 2011, at 6:01 PM, Oleksandr Moskalenko
o...@hpc.ufl.edumailto:o...@hpc.ufl.edu wrote:
I need to get Galaxy to use tools that are not located in the system path. At
the command line I can export the PATH either manually or with environment
modules
Ann Black wrote:
I figured out a solution. The sun grid engine will strip back the env of
what gets passed along with the job submission. I added a native drmaa
option, -V, which caused the env vars found on the shell that submits the job
to be passed along. Therefore all the environment
on this ASAP.
Thanks,
Jeff
On Sep 6, 2011, at 10:18 AM, Nate Coraor wrote:
Whyte, Jeffrey wrote:
Thanks for the information, Nate.
I installed Python as you described, and the error I get now is pasted
below. I appreciate your help.
Jeff
[~/galaxy-dist] myuserid
Timothy Wu wrote:
Thanks, this helps. I was running with an interpreter and I didn't realize I
had to had the full path in there. I was expecting that $PATH which contains
the directory the script was located in to take care of it. Thanks you very
much for the clarification.
If the script is
Trevor Wennblom wrote:
On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote:
This is normal since OS X has binary compatibility with older releases,
the Python distributors build for an older platform rather than each
individual platform.
I see there's now an Intel-only build for 10.6
Edward Kirton wrote:
In your position I agree that is a pragmatic choice.
Thanks for helping me muddle through my options.
You might be able to
modify the file upload code to gzip any FASTQ files... that would prevent
uncompressed FASTQ getting into new histories.
Right!
I
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, September 02, 2011 1:40 PM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] rpy - No module named rpy CentoOs install
Joseph Hargitai wrote:
additional info
, the operation does not work and there is a link with this stuff :
http://bytes.com/topic/python/answers/26169-shutil-move-error-errno-17-file-exists-win32
- Regards
2011/9/2 Nate Coraor n...@bx.psu.edu
remy d1 wrote:
Hi,
We found a little problem in the new galaxy release. When
report back with the output of:
% python ./scripts/get_platforms.py
?
Thanks,
--nate
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, September 02, 2011 1:16 PM
To: Whyte, Jeffrey
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev
Nikhil Joshi wrote:
Hi all,
Is there a repository of pre-indexed genomes for base-space/color-space,
bwa, bam, sam, etc...? It would be much easier than having to index them
all ourselves :)
Hi Nik,
I've been meaning to set this up for a while now. Stay tuned for an
announcement once
Kristen Eisenberg wrote:
[galaxy-dev] Failure to prepare job error
Hello,
I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I
import a package I've installed called PypeR. My tool works fine from the
command line, but when I try to run it on my Amazon instance, it
Timothy Wu wrote:
Hi,
I'm trying the add tool tutorial at
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
how do I designate the path of the tool if it's not dropped into the same
directory as the tool config xml? Some executable may not be in the
directory.
SHAUN WEBB wrote:
Hi.
I am interested in putting quotas in to effect on our local Galaxy
server. From the admin page I can create a quota but this only seems
to apply to disk space. I noticed on your test site you have quotas
for concurrent jobs also. Have I missed how to set this or is
Peter Cock wrote:
On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor n...@bx.psu.edu wrote:
Edward Kirton wrote:
Peter wrote:
I wonder if Galaxy would benefit from a new fastqsanger-gzip (etc)
datatype?
However this seems generally useful (not just for FASTQ) so perhaps a
more
Roxanne Tapia wrote:
Hi,
I was going through the examples in the README, and everything went along
fine until I tried to upload files from the import directory:
usage: library_upload_from_import_dir.py key url folder_id file_type
server_dir dbkey
I don't understand what the last two
Peter Cock wrote:
On Thu, Sep 1, 2011 at 9:00 PM, Trevor Wennblom tre...@well.com wrote:
...
given that python has syntactically significant whitespace, i also
try to maintain the convention of indentation with four-spaces.
i've noticed this isn't consistent within the codebase, but does
Joseph Hargitai wrote:
additional info:
it is possible on the same node to run manually
./gsummary.py
with the header:
#!/usr/bin/env python
import sys, re, tempfile
from rpy_options import set_options
set_options(RHOME='/apps1/R/2.13.1/intel/lib64/R')
from rpy import *
Where
Hi Nikolai,
It's best to send questions directly to the mailing list, so they reach
the widest audience and the right people.
There are some responses below:
Nikolai Vazov wrote:
Hi, Nate,
You helped me install Galaxy with a DB hosted on a remote server via
SSL connection. Thanks a lot
remy d1 wrote:
Hi,
We found a little problem in the new galaxy release. When we upload a
dataset library from filesystem :
Admin Manage data libraries create new data library Add dataset
Upload files from filesystem path Link to files without copying
If galaxy user is the owner of
Whyte, Jeffrey wrote:
Hi,
I've been having trouble running a local instance of Galaxy on a Mac Pro
after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and
Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed.
The error I see after running the startup
Edward Kirton wrote:
hi, we are getting the following error migrating from 79 to 80.
curiously, my own galaxy didn't have this problem, but another
developer here was getting this error. i moved him from sqlite to
postgres but that didn't help.
thanks for any assistance,
ed
Hi Ed,
Is this
Sarah Diehl wrote:
I just also found out about this bug (or feature). It is exactly the
same for me and I'm running an older Galaxy version (galaxy-dist
from April 8, 2011).
Hi Sarah, Alex,
Dannon fixed this bug back in July, in changeset 5814:ebb1014b237d,
which is now available in
Louise-Amélie Schmitt wrote:
Hello everyone,
I'm currently trying to automate data loading and pre-processing
through Galaxy's API, and I will need to delete and share histories
at some point. I know the API is still very new but is there a way
to do that by any chance?
Hi L-A,
As of last
Shantanu Pavgi wrote:
Hi,
There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What
is involved in this step? Is it run for every dataset/output being generated
in the galaxy?
Hi Shantanu,
Metadata is always detected/set on all job outputs. This setting simply
some time.
Best,
L-A
Le 23/08/2011 19:49, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hi,
I would need to make a tool that can get the API dataset id out of
the input dataset of the tool, how can I do that?
Hi L-A,
Pass in as an argument:
$__app__
Shantanu Pavgi wrote:
On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote:
Shantanu Pavgi wrote:
Hi,
There is a 'set_metadata_externally' setting in universe_wsgi.ini file.
What is involved in this step? Is it run for every dataset/output being
generated in the galaxy?
Hi
Louise-Amélie Schmitt wrote:
Le 30/08/2011 16:51, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
I just changed it and ran into an error, so I modified the line and
it now works fine:
$__app__.security.encode_id( '%s' % $input1.id )
What was the 'file.' originally for?
On the API side
Jack Zhu wrote:
Hi all,
I have problems with updating my local instance of Galaxy.
Specifically I can not migrate the database schema from 80 to 81:
Hi Jack,
Thanks for reporting this issue. It has been fixed in changeset
5951:62d51750d7df.
--nate
--
$$ sh manage_db.sh
.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
python
2.6 (EPD version 6.1-1)? I get this error which I suspect is related to
the
fact that I have EPD python
Louise-Amélie Schmitt wrote:
Hi,
I ran into a little something that is a bit annoying for debug when
trying to upload files through the API with
library_upload_from_import_dir.py. When the specified folder is
wrong, python tries to process the error tuple like a dict, so the
original error
paul.tan...@colostate.eduwrote:
It is free for academic use. I'll try what you suggested below - thanks!
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it
working
with EPD python
DistributionNotFound(req) # XXX put more info here
pkg_resources.DistributionNotFound: numpy==1.6.0
Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger
Louise-Amélie Schmitt wrote:
Le 29/08/2011 15:52, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.
Why use API keys instead of user names? Is it to to prevent anyone
/get_platforms.py
? Note that this needs to have the path changed from append to insert
as in the previous scripts.
Thanks,
--nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6?
error returned
scrambling pysam as instructed below and see
what the results are? You will have to do this for each egg that can't
be downloaded.
--nate
On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger wrote:
That worked, for everything but pysam. I also tried
Hi Ilya,
Sorry, I haven't yet had a chance to check out your code. Are you using
the username column of the user table to determine the local username?
This would then be job.user.username.
--nate
Chorny, Ilya wrote:
So I figured out that it is job/runners/__init__.py that does the cleanup.
Crystal Goh wrote:
Hi, I am Crystal.
As Tophat for SOLiD only available in Galaxy Test (not available in Galaxy
Main), I uploaded my csfasta and qual files to Galaxy Test. As the file size
very big, the disk space used up is 13.5Gb and I cannot use any tool. This
means after uploading
Edward Kirton wrote:
i thought i recalled reading about downloading files from a history
via ftp, but i could been mistaken -- couldn't find anything on the
wiki or mailing list archives. does this feature exist?
what's the best way for users to download many or large files other
than via
Hi Iry,
By default, PasteScript is looking for a section named [server:main].
With this config, you can start the servers with:
% sh run.sh --server-name=web0
% sh run.sh --server-name=web1
% sh run.sh --server-name=web2
--nate
Iry Witham wrote:
I have performed a new install of
Chorny, Ilya wrote:
I noticed that when uploading multiple files only one job gets submitted to
the queue. Is there a way for galaxy to split that up on multiple nodes?
Not at present, no. Which upload method are you using? This is
probably something that could be done for certain types
Zhibin Lu wrote:
Hello,
When i try to upload bam files into galaxy data library though
system paths with link to files without copying into galaxy
option, galaxy always complains that
The uploaded files need grooming, so change your*Copy data into
Galaxy?*selection to be*Copy files into
Edward Kirton wrote:
also, delete and purge a quota seems to have no effect.
Hi Ed,
They work for me. Note that delete/purge do not actually delete the db
row itself.
Delete marks the quota as deleted, and it no longer counts against any
associated users. Purge removes all of the user/group
Joseph Hargitai wrote:
Hi,
built a new server today to test a few things.
a, Help is not clickable via Apache2 proxy
2, when you use an apache2 proxy is it for granted that local authentication
cannot be used? I tired
remote-user = False
hoping i can use load-balancing and proxy
501 - 600 of 764 matches
Mail list logo
