or
stayed the same and so far I have just seen it in the context of toolshed
operations. I don't know what else I could do to ensure proper encoding.
Best regards,
Sarah
- Original Message -
From: "John Chilton"
To: "Sarah Diehl"
Cc: "galaxy-dev@lists.b
Dear all,
I'm trying to migrate our local Galaxy server from a standalone server running
on CentOS 5 to a setup that runs Galaxy in a Docker container
(bgruening/galaxy-stable). Due to Docker and the setup of the container, almost
all data, tools, configs etc. have to move to a different place.
Hi everyone,
I uploaded a bunch of files to the Galaxy data libraries with the option
"Upload files from filesystem paths" and "Link to files without copying to
Galaxy". Afterwards I edited the names that are displayed in Galaxy. However,
now the files are not alphabetically sorted anymore. I t
Hi everyone,
is anybody using the user information form feature
(https://wiki.galaxyproject.org/Admin/Config/User%20Information)? For me it
does not seem to be working. I created a form as explained on the wiki page,
but nothing changed in the user registration. It just causes an internal serve
Hi Nate,
thanks for all your help! I attached the full installation log file.
Best regards,
Sarah
- Original Message -
From: "Nate Coraor"
To: "Sarah Diehl"
Cc: "galaxy-dev@lists.bx.psu.edu List"
Sent: Tuesday, February 25, 2014 3:57:36 PM
Subjec
ginal Message -
From: "Nate Coraor"
To: "Sarah Diehl"
Cc: "galaxy-dev@lists.bx.psu.edu List"
Sent: Friday, February 21, 2014 5:10:46 AM
Subject: Re: [galaxy-dev] Error when installing package_galaxy_utils
Hi Sarah,
This looks a lot like a transient filesystem
Hi everyone,
I just updated our local Galaxy installation to the latest dist version and
also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh).
However, the package galaxy_utils gave me an error and I don't have the
slightest idea what happened. So any help to figure out the
Hi everyone,
in my job_conf.xml I defined the following limit
536870912000
Galaxy seems to correctly identify the number as 500 GB, since I got the error:
"Job output file grew too large (greater than 500.0 GB), please try different
inputs or parameters"
The problem is that the output file of
Hello everyone,
any news on this bug? I have the same issue here, with the error
TypeError: column_types is undefined @
http://galaxy.immunbio.mpg.de/static/scripts/mvc/data.js:188
The suggested fix works for me, but the resulting formating isn't nice.
Best regards,
Sarah
- Original Messag
Hi all,
it seems my clean-up enthusiasm caused some inconsistencies with datasets'
deleted status. I encounter the following phenomenon: datasets appear totally
fine in the data libraries, but once they are loaded into a history, they
appear as deleted there.
I dug through the database and fou
Ok, sorry for having bothered you again with my stupidness... I actually have a
test instance of galaxy on the same server with the database directory
hard-linked. After I deleted that one the space was free *d'oh*.
- Original Message -
From: "Sarah Diehl"
To: &q
space: 9515493164336
Elapsed time: 5669.43398285
So the freed disk space should be around 9 TB, right?
Best regards,
Sarah
- Original Message -
From: "Hans-Rudolf Hotz"
To: "Sarah Diehl"
Cc: "galaxy-dev@lists.bx.psu.edu List"
Sent: Thursday, February 28, 2
Hello,
our Galaxy server is running low on disk space, so I asked all users to
(permanently) delete old histories and datasets. One specific user alone
managed to reduce his space usage by 2 TB. That's at least what the Galaxy
server says. Afterwards I additionally ran the following scripts:
d
Sarah
- Ursprüngliche Mail -
Von: "Nate Coraor"
An: "Sarah Diehl"
CC: "galaxy-dev@lists.bx.psu.edu List"
Gesendet: Dienstag, 19. Februar 2013 17:59:24
Betreff: Re: [galaxy-dev] Datasets linked into Galaxy do not work
On Feb 14, 2013, at 4:38 AM, Sarah Diehl wrot
Hi Nate,
copied datasets do work and I run Galaxy from the server root.
Thanks,
Sarah
- Original Message -
From: "Nate Coraor"
To: "Sarah Diehl"
Cc: "galaxy-dev@lists.bx.psu.edu List"
Sent: Wednesday, February 13, 2013 8:22:10 PM
Subject: Re: [galaxy-de
Hi all,
I have problems with datasets that were linked into Galaxy data libraries (as
Admin: "Add datasets", select "Upload files from filesystem paths" and "Link to
files without copying to Galaxy"). Those files cannot be looked at, downloaded
or viewed in a genome browser.
Errors in the brow
So, I fixed the problem myself ;-). For whatever reason the files need to be
owned by the galaxy user. I achieved that by setting
SQLDefaultUID 501
SQLDefaultGID 501
in the proftpd.conf. 501 is the UID and GID of the galaxy user and group.
- Original Message -
From: "Sarah
Hi everyone,
my local installation of Galaxy has an issue with using the "Upload File" tool
on data that was uploaded to the ftp server. The ftp upload itself works fine:
-rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa
but there seems to be some issue with Galaxy moving it and I have
Hello all,
one of my users encounters a strange error with the GATK tool "Unified
Genotyper". At the end of the message you see the original error report. The
problem there was that the reference genome is missing. The tool was run as a
part of a bigger workflow, but I double checked the workfl
ueue' object has no attribute 'job_lock'
Regards,
Rem
2012/6/7 Edward Kirton < eskir...@lbl.gov >
yes, i've had the same error ever since the last galaxy-dist release. i
previously had multiple servers and switched to the one manager, two handlers.
rewrite rules
Hi all,
I have a similar, maybe related problem. I'm running a configuration as
described at
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling.
I have three webservers, one manager and two handlers. Everything is
behind an Apache and the rewrite rules are set acco
iki should provide the information you
need. Let me know if you bump into any additional questions.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel
Thanks!
Greg Von Kuster
On May 24, 2012, at 8:15 AM, Sarah Diehl wrote:
Hi all,
currently I face some strange
Hi all,
currently I face some strange behaviour of the tool panel in Galaxy if I
add top-level label tags to the tool_conf.xml. The problem is that the
labels stay forever, even if I remove them again from the tool_conf.xml
and they also appear three section earlier than where I put them.
I tr
Thanks Peter! It's very likely that I have the exact same problem,
because I also have CentOS and needed to compile Python.
On 05/22/2012 05:04 PM, Peter Cock wrote:
On Tue, May 22, 2012 at 3:30 PM, Sarah Diehl wrote:
Hi all,
today I updated my test server to the newest galaxy-ce
Hi all,
today I updated my test server to the newest galaxy-central version.
However, when I start it, I get the following error:
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in
command.run()
File
"/galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/
Hi Jeremy,
I was able to reproduce the error on the public Galaxy server. I shared the
history with you (jeremy.goe...@emory.edu). It's named "export history to file
bug".
Thanks.
Sarah
- Original Message -----
From: "Sarah Diehl"
To: "Jeremy Goecks"
r workflow?
Thanks,
J.
On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5
with flavor: Numerical sort
everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks,
J.
On
Sort (version 1.0.1)
on column: c5
with flavor: Numerical sort
everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks,
J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive
HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/"; "Mozilla/5.0 (X11; U;
Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.f
Hi everybody,
how up-to-date is http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP?
I just set up a ProFTPd according to those directions, but had to change
some things, especially regarding permissions of directories and files.
I had to set
Umask 000
CreateHome on 755 dirmode 755
Al
Hi all,
is there some way I can allow datasets (specifically bam files) that are
annotated with a custom build to be displayed in a local IGV (assuming a
genome with the same name was generated for IGV)?
I tried some things with display_applications/igv/bam.xml, but I
couldn't get it to work
h
Sorry for the inconvenience - I'll get this fix out as soon as I
possibly can. Let me know if you bump into any problems with this.
Greg Von Kuster
On Feb 24, 2012, at 10:42 AM, Sarah Diehl wrote:
Hi all,
I just updated our Galaxy from the latest dist to the latest central
release. W
Hi all,
I just updated our Galaxy from the latest dist to the latest central
release. When I had previously updatet to the dist release, the emboss
datatypes were installed as a shed tool. However when restarting the
server after the update the datatypes_conf.xml in the emboss shed
directory
Hello,
one quick question: is there a way to get news about new tools in the
Tool Shed?
I saw that I can subscribe to get news about already existing tools, but
how about newly created ones? I would also be fine with some
subscription to any changes in the Tool Shed in general.
Best regard
I'm only guessing here, but maybe the issue is that the parameter names
are all the same (namely "model"). Did you try with only unique names?
Especially this one:
should get it's own name.
Sarah
On 02/06/2012 03:38 PM, Holger Klein wrote:
Dear all,
I'm working on a tool wrapper which f
Ok, I found the problem myself. I was totally searching in the wrong
place for the error. It was simply a syntax problem. The output
definition should be like follows:
I was closing the data tag too early.
On 10/06/2011 11:40 AM, Sarah Diehl wrote:
Hello,
I'm trying to wr
Hello,
I'm trying to write a wrapper for the intersectBed tool from the
BEDTools suite. The difficulty lies in the possible combinations of
input and output data formats. Input can be either bed or bam. When the
input is bed, the output is also bed. However, when the input is bam the
output c
is related to a bug we're
currently looking into. If you run it again, does it have this error
consistently or does it only happen once in a while?
Thanks,
K
On Thu, Jul 7, 2011 at 12:11 PM, Sarah Diehl <mailto:di...@immunbio.mpg.de>> wrote:
Hi everybody,
Hi Gus,
for parameters of the type "select" you can enable the option to select
multiple options. However, this isn't really suitable for files, I think.
I recommend to use the repeat tag (see
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the
existing parameter to make
ution within the next few weeks. Thanks for finding this.
Greg Von Kuster
On Jul 8, 2011, at 3:53 AM, Sarah Diehl wrote:
Hello,
when I go to the user preferences and try to change the default permissions for
new histories, I always get the following error (full message in attachment):
Hello,
when I go to the user preferences and try to change the default
permissions for new histories, I always get the following error (full
message in attachment):
Error - : set_default_permissions() takes
exactly 3 non-keyword arguments (2 given)
URL: http://solweb2.immunbio.mpg.de/user/s
Hi everybody,
when I run the build_profile_indexes.py script in the
scripts/tools/annotation_profiler/ directory on hg19 (downloaded
yesterday from UCSC), I get the following error:
Created table dir
(profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal).
['fileName']
Ta
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).
On 07/06/2011 09:32 PM, Bossers, Alex wrote:
In our local instance (central version) up to changeset (June 28th) I noticed
in the admin p
Hi Peter,
thank you very much for your help! I guess the Galaxy version we are
currently running is about two months old. I really need to update...
Best regards,
Sarah
On 07/04/2011 03:04 PM, Peter Cock wrote:
On Mon, Jul 4, 2011 at 1:46 PM, Sarah Diehl wrote:
Hello,
in the config of a
Hello,
in the config of a tool I want to integrate into Galaxy I would like to
have a parameter with the following properties:
min="10" max="100" />
So it should be possible to leave this field empty, but when you choose
to enter a number it should be between 10 and 100.
The problem now i
Hello everybody,
currently I have some trouble with the following kind of error:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position
155: ordinal not in range(128)
We have encountered it twice now. The first time it was related to a
shared library, which could not be opened
Hello everybody,
I just found out that there was a major update to cufflinks on 5/5/2011.
At least for us it now makes no sense anymore to use the old version,
besides the fact that the cufflinks team highly recommends upgrading.
Does anybody already have new wrappers for all the cuff... tools
g the masthead in your browser should solve the problem. By "masthead", I mean
the following - right click on it and select "Reload page", or whatever your browser
provides for an option:
On Apr 15, 2011, at 8:31 AM, Sarah Diehl wrote:
Hello,
it seems since I updated to
y',
line 80 in __call__
return self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line
632 in __call__
return self.application(environ, start_response)
I could narrow it down even further. As soon as I set anything to "To be
set at runtime" the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a
screenshot of a really simple workflow whose down
dev.
Thanks,
J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list
(http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when
trying to download a workflow.
Were you able to find a solu
o the file?
Best regards,
Sarah Diehl
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Hello Yu,
first, you need to change the /home/nate/galaxy_dist in the rewrite
rules to the directory on your machine where the galaxy files are.
Second, I think the apache user needs at least read access to the static
directory inside the galaxy directory.
Regards,
Sarah
On 04/12/2011 04:1
Hi Isabelle,
thank you for your help. However filter-with=gzip is disabled in our
configuration. I set everything according to the guide on
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer. The
gzip option you see in my log is from the Apache server.
Sarah
On 03/10/
Hi all,
I encounter the same error that was already mentioned in this list (with
the same email title). For me it also does only happen when debug is set
to false. However I could not find a solution to it in the archive of
the mailing list. I tried it with both galaxy-dist and galaxy-central,
) and then
it compiled against the new R version.
Best regards,
Sarah
On 03/03/2011 05:11 PM, Nate Coraor wrote:
Sarah Diehl wrote:
Hi all,
I'm currently working on setting up a fresh Galaxy server at our
institute. I'm going through the tool dependencies list and install
ever
c:/progra~1/r/rw2011/')
>>> from rpy import *
It looks like my version of R isn't supported by rpy. Does anybody know
which version of R still works with rpy? I couldn't find anything about
it. What about rpy2? Is it not supported by Galaxy?
Thanks very much in a
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