On 01/25/2011 03:44 PM, Davide Cittaro wrote:
On Jan 25, 2011, at 3:40 PM, Hans-Rudolf Hotz wrote:
Hi Davide
We were in a similar situation when we switched to external authentication.
Although, only one user was affected and we were using MySQL.
I could fix it by changing the contents
On 02/21/2011 04:05 PM, Branden Timm wrote:
Hi All,
My group is trying to create some custom sections in the Tools pane, and
have run into an issue. We have a custom section, within which there are
three different labels and several tools under each label. We are trying
list the same tool
the time required to teach
the use of Galaxy in general and the use of the self-written tools to
your colleagues at the bench.
Regards, Hans
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
I should
On 04/07/2011 11:40 PM, Ryan Golhar wrote:
Hi all - So, I been asked to provide specs for a production Galaxy
system to support approximately 20-30 users. Most of these users are new
to bioinformatics and very new to NGS. I'm targeting a user base that
will use a light to moderate amount of
On 04/12/2011 09:20 AM, hari krishna wrote:
Hi,
Thanks for your immediate reply,
ya same thing i tried but i cant able to open that page.. giving
error as cant able to locate http://your host:different port number/
address is coming .
my be i did wrong at
On 04/14/2011 07:36 PM, Greg Von Kuster wrote:
Hello Louise,
I've CC'd Nate on this as he may be able to help - although no guarantees. I'm
not expert enough in this area to know where to look for the cause. Perhaps
someone in the community can help as well.
It is likely that LDAP is
On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote:
Hi Hans, thanks for your reply.
- is your PostgreSQL database in sync with the database folder?
I'm sorry I'm not sure I get what you mean, what folder is it?
the folder where you keep the datasets, eg:
your local
with supposedly nonexistent
histories.
Thanks again
L-A
Le vendredi 15 avril 2011 à 13:47 +0200, Hans-Rudolf Hotz a écrit :
On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote:
Hi Hans, thanks for your reply.
- is your PostgreSQL database in sync with the database folder?
I'm sorry I'm
Hi David
Have you looked into the excellent Galaxy Unix-Tools package created
by Gordon Assaf?
http://hannonlab.cshl.edu/galaxy_unix_tools/index.html
The Find Replace text in line/column tool is probably what you are
looking for:
Hi Ed
You can use the variable $userEmail in the 'command' tag of the tool
definition file
Regards, Hans
On 05/06/2011 03:56 AM, Edward Kirton wrote:
is there a variable i can use in the tool config xml file?
thanks!
ed
___
Hi Darren
I assume, you have created a new data type
https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes
You can now disable the 'sniffing' by adding the data type to the
following line:
unsniffable_binary_formats = [ 'ab1', 'scf' ]
in:
Hi Harendra
I am not aware of anybody who made this kind of transition without
running into all kind of problems. I suggest the following workaround:
- set up a new, independent Galaxy server using PostgreSQL.
- transfer the histories you want to keep to the new server using the
'Export to
Hi
we are looking into different methods to display dynamic contents in the
tool user interface.
To start, we looked at the 'Operate on Genomic Intervals:Profile
Annotations' tool. We turned it on in a local installation (May 20,
8c11dd28a3cf release), but we struggled to get the interface
On 06/09/2011 02:47 PM, Arun Selvam wrote:
Hi,
I am new to galaxy, I just downloaded and installed galaxy on my MAC
system. I also download bowtie , and it is working perfectly on the
command line. But am not able to see the bowtie option under mapping
in the galaxy menu.
Are you sure,
Hi Ryan
Our sysadmin spent quite some time on this problem...in the end, he gave
up and installed R 2.9.0 on our new server.
So, we ended up with two versions of R: one is used for rpy (we define:
R_HOME=/***/***/galaxy/helpers/R/R-2.9.0 in the 'run.sh' script), and
an up-to-date version of
Hi Colin
In your 'universe_wsgi.ini' file, have you changed the line:
library_import_dir = None
to the directory with your data?
Regards, Hans
On 06/28/2011 11:38 AM, colin wrote:
Hi,
i all, my first post in the mailing list. I started one moth ago galaxy (at the
conference) and the
On 06/28/2011 01:50 PM, colin molter wrote:
hi,
no, i found that just later and that solved the problem. i wanted to cancel
my question .. but too late.
anyway i managed to put my 35Gb fastq files on galaxy and i am transforming
it whith the fastq groomer.
any idea about the other problem
Hi Colin
I launched a big job on my local galaxy server (for which I am admin). The job
was to put local dir in the datalist.
It took too long and i wanted to stop it but how?? i failed to find a
solution.
go to the admin view - 'Manage jobs' and there you can kill individual
jobs.
On 06/28/2011 07:06 PM, colin molter wrote:
hi hans,
you are right.
it seems that even if i stopped galaxy
(i just stopped the run.sh command)
i still have a job running:
root 10441 97.0 0.0 77496 1772 pts/6R11:59 402:48 python
/opt/galaxy-central/tools/fastq/fastq_groomer.py
Hi Paul
You probably need to be a bit more specific...at what stage is this
'.txt file' read (or rather should be read)? - are you offering the
(growing) list of databases as options to select in the GUI?
Hans
On 06/29/2011 10:20 AM, Admins de Galaxy wrote:
Hello everyone,
we have a
Hi Paul
Please keep all replies on the list by using reply all
A simple solution, which we use quite a lot, is the following:
we use the dynamic_options attribute, eg:
inputs
param name=foo type=select label=what
help=Use tickboxes to select
display=radio
display an interface.
If you would like to use or run the tool, you may find
$GALAXY_ROOT/scripts/tools/annotation_profiler/README.txt helpful. Please let
us know if you encounter further difficulties.
Thanks for using Galaxy,
Dan
On Jun 8, 2011, at 8:10 AM, Hans-Rudolf Hotz wrote:
Hi
we
Hi Luobin
It is difficult to guess without seeing your code.
So, assuming you followed the steps described in the wiki
(http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes), I guess
you just made a typo somewhere (since this has happen to me several
times when adding a new
Hi
I apologize, if this problem has already been solved/discussed. I went
through the e-mail repos, but couldn't find anything.
With a little delay, I am in the process of upgrading our local Galaxy
server. Currently, I am running a few tests with the June 23, 2011
(720455407d1c) release.
tag.
Branch
25 days ago
On Aug 16, 2011, at 10:38 AM, Hans-Rudolf Hotz wrote:
Hi
I apologize, if this problem has already been solved/discussed. I went through
the e-mail repos, but couldn't find anything.
With a little delay, I am in the process of upgrading our local Galaxy server
Hi
I am pretty sure, this must have been discussed before, but again, I
cannot find a hint/reference in the e-mail archive:
If I install a new galaxy server using the June 23, 2011 release
(changeset: 5743:720455407d1c), I cannot save a visualization after
adding a new track:
I get a
Hi
I am sorry to be a pain in the neck, but as part of our quarterly
upgrade procedure, I am stumbling across the next problem:
Can anybody confirm, that the visualization does not work with the
June 23, 2011 release (changeset: 5743:720455407d1c) when using IE8
or IE7 on windows XP?
(it
On 08/25/2011 12:12 PM, Nikhil Joshi wrote:
Hi all,
Is there a relatively easy way to create your own input/output formats?
Some of the formats from programs that I am trying to install on our local
Galaxy do not exist as an option. Any ideas?
Hi
have you looked at the following wiki
Hi
The option to filter a BED file by the score in the visualization tool
is brilliant! There is just one draw back: you can only filter by
integers. Hence a score of 1.1 is the same as of score of 1.3.
How difficult would it be to change the code in order to allow floats
for the filter?
On 09/14/2011 10:39 AM, Timothy Wu wrote:
//
Alternatively, I can just ask user to download from NCBI ftp themselves,
decompress them, and upload it to galaxy.
What's the best approach here?
How about: you download the data once, and then offer it as a 'data
library' to your users. This
Hi
just asking the obvious questions to double check:
- are you sure, this second instance is not accessing the same
PostgreSQL/MySQL database as the first one?
- are you sure, the user you are logged-in does exist in the
PostgreSQL/MySQL database? I kind of remember getting a similar
Hi Timothy
Are you talking about the name as it will appear in the history?
Then have a look at the following wiki page:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set
Regards, Hans
On 10/12/2011 10:50 AM, Timothy Wu wrote:
Hi,
I thought I had already
Hi Timothy
I don't really see the connection to you first question, but maybe I
misunderstood the first one
Anyway, you probably need to define those output files which are
required by B as 'Static Multiple Outputs' and the rest as 'Variable
Static Outputs determined by parameter
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.
Regards, Hans
On 10/25/2011 10:38 PM, Andrew Warren wrote:
When
Hi Shantanu
Sorry, for replying so late (I am working down a pile of e-mails which
accumulated during my holidays).
I have just implemented your suggested changes in our dev server. It is
brilliant - Thank you very much!
I will do it for our production server within the next few days.
Hi Allessia
It is difficult to help you without knowing what kind of error you've
got.
What is the error message you get?
Regards, Hans
On 10/31/2011 03:35 PM, Alessia D wrote:
Hi,
I am very new to Galaxy and so far have only used the online interface.
However, I have an old
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL)
database.
Before copying your existing Galaxy server, you might wanna start with
running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08
wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a rookie Galaxy user,
So may you pls explain me in details the meaning by running a second Galaxy server
in parallel using a fresh check-out ?
Thank a lot for your assistance!
Liram
-Original Message-
From: Hans-Rudolf
the
databases.
But how can I separate between them?
Thanks you!!
Liram
-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Wednesday, December 21, 2011 4:59 PM
To: VARDI,LIRAM (A-Labs,ex1)
Cc: galaxy-...@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1)
Subject: running two Galaxy installations
the relational databases and making sure the file systems for your two
servers are really separate from each other.
Hans
Thanks,
Liram
-Original Message-
From: Fields, Christopher J [mailto:cjfie...@illinois.edu]
Sent: Thursday, December 22, 2011 4:50 PM
To: Hans-Rudolf Hotz
Cc: VARDI
On 01/09/2012 05:04 AM, Vidya .H.K wrote:
Hi,
I am new user to galaxy. I have installed galaxy on the Linux local server
for ChIP-seq analysis. While running MACS, an error is flagged
An error occurred running this job: /bin/sh: macs: not found .
I have set the path for macs in /bin. But
On 01/10/2012 06:31 AM, Vidya .H.K wrote:
Hi,
I think macs is exceutable with galaxy user.
what happens if you execute macs_wrapper.py on the command line?
Regards, Hans
PS: Please send all follow-up with a cc to the mailing list (reply-all).
On 01/09/2012 05:04 AM, Vidya .H.K
Hi
Have you looked into using Data Libraries, see:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
you get access to the data without duplication.
Regards, Hans
On 01/17/2012 12:35 AM, Joshua Gross
Hi
I am in the process of upgrading all our Galaxy servers to the current
changeset (b258de1e6cea, Nov. 18) and I have noticed an inconsistency:
If I upgrade one of our old servers (which was on 720455407d1c, June
23) with 'hg pull -u -r b258de1e6cea' I get the following:
Regards, Hans
Thanks,
J.
On Jan 18, 2012, at 9:19 AM, Hans-Rudolf Hotz wrote:
Hi
I am still in the process of upgrading all our Galaxy servers to the current changeset
(b258de1e6cea, Nov. 18) and now I am running into troubles with the
visualization:
Depending on the location
Hi Jeremy
Thank you very much for your help. I will look into your suggestions.
Regards, Hans
On 01/18/2012 10:08 PM, Jeremy Goecks wrote:
it works fine on the public server
Good, this narrows down the problem to installing the -central script on your
instance b/c main's copy of the
Coraor wrote:
Hi Hans,
We're releasing a distribution today. If this is still the case with that
distribution, let me know. There were branches that weren't showing up under
newer versions of Mercurial. Hopefully this is all resolved in the latest.
--nate
On Jan 17, 2012, at 4:11 AM, Hans-Rudolf
On 01/22/2012 01:41 AM, Anthonius deBoer wrote:
All tools need to be in the path of the user running galaxy.
but can be simply added to the path by adding them to the 'run.sh' script
Regards, Hans
Regards,
Thon
Thon de Boer, Ph.D
Bioinformatics Guru
T: +1.650.799.6839 | E-mail:
As I wrote in my previous e-mail: Please send all follow-up with a cc
to the mailing list (reply-all).
In order to debug you situation you need to simulate a complete
commandline, the same Galaxy is doing.
Regards, Hans
On 01/23/2012 05:35 AM, Vidya .H.K wrote:
Hi,
Sorry for delayed
Hi
The recently added new function allowing administrators to impersonate
other users is a really useful tool - thank you very much.
It works great on our development server. Unfortunately, it does not
work on our production server which relies on external authentication
via Apache. Is
Hi Nate
Yes, upgrading one of our old servers with hg pull -u -r 63bc46cc73b7
and downloading a new clone with hg clone
http://www.bx.psu.edu/hg/galaxy galaxy-dist, does not result in the
same changeset number (ie '6528')
Thank you very much
Hans
On 01/20/2012 09:04 AM, Hans-Rudolf Hotz
On 01/24/2012 06:19 AM, Vidya .H.K wrote:
Hi,
Actually I am not computer expert as well. I have just started to work in
this area. so I am not able to figure out how to solve this problem. I
request you to elaborate on what you meant in your previous mail.
by simulating a complete command
On 01/24/2012 10:27 PM, Kim, Hyunsoo wrote:
Hello,
I have local instance of galaxy and wanted to modify “upload file” so
that I will be able to upload large files ( 2GB).
The reason I am trying to do this in browser is that extra tools for FTP
do not really work in my environment because of
that regular users can upload large files through Galaxy's
GUI without external FTP tool.
Thanks,
Hyunsoo
-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Wednesday, January 25, 2012 4:02 AM
To: Kim, Hyunsoo
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Uploading
Hi Alex
Since you are talking about your public server, I assume you don't have
external authentication. Hence, have you considered to turn on the
allow_user_impersonation option?
Nice and very efficient way of cleaning up.
Regards, Hans
On 01/27/2012 10:43 PM, Bossers, Alex wrote:
Hi Nate
Sorry, this was a typo, I meant to write: does noW result in the
same changeset number (ie '6528') - so everything is fine now.
I apologize for the confusion
Hans
On 02/01/2012 07:13 PM, Nate Coraor wrote:
On Jan 23, 2012, at 8:01 AM, Hans-Rudolf Hotz wrote:
Hi Nate
Hi
I guess we see similar things: a new history item is created, it turns
purple, stays like this apparently forever while no job id is created
(ie I don't see the job in any of the report tools).
To be honest we ignore them, because:
a) it only (as far as I can tell) happens with big data
Hi Victor
Have you looked at the wiki page:
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files
Variable Static Outputs determined by parameter values is probably
what you want
Regards, Hans
On 02/24/2012 10:16 PM, Victor Ruotti wrote:
Thank you Shaun.
That worked really
Hi Keith
It works with dropdowns and the when tag set on the same interface
page, see:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cwhen.3E_tag_set
Regards, Hans
On 02/29/2012 07:11 PM, Keith Sheppard wrote:
Hello, From looking at the documentation for tool config
Hi Leandro
Although we use 'dynamic_options' successfully in many tools, it is
still a little mystery to me sometimes - probably due to my non-existing
python knowledge.
Hence just double checking:
Does [ One,1,True ],
[ Two,2,False ],
[ Three,3,False]
Hi everybody
This is kind of an embarrassing question, but I am struggling to get the
display at UCSC to work.
Finally after several years, our sysadmin agreed to change the Apache
configuration (which handles the authentication via LDAP) according to
the configuration provided in the
Hi Huayan
I got a silly question for you. My galaxy is running now but I'd like
to customize it.
I've changed the welcome.html page but the galaxy mirror site is
showing the old one. Do I need to change some other files or other
configurations?
Are you sure the page is not cached locally?
):
~/galaxy_dist/static/welcome.html
~/galaxy_dist/tool_conf.xml
~/galaxy_dist/tool_conf.xml.sample
and restart the server? the missing tool_conf.xml should cause the
start-up to fail
Regards, Hans
Best,
Huayan
On 8 Mar, 2012, at 10:52 PM, Hans-Rudolf Hotz wrote:
Hi Huayan
I got a silly
On 03/19/2012 10:19 PM, Peter Cock wrote:
On Mon, Mar 19, 2012 at 8:41 PM, Mark Johnsonmjohn...@ncbi.nlm.nih.gov wrote:
I'm writing some tools to integrate NCBI data resources with Galaxy. I have
two questions.
The first is simple. I want to write a tool for a long-running process that
is
Hi Jan
This is brilliant - it is always the simple solutions you overlook -
thank you very much!
May I just add a modified version, in case you use external
authentication. There is no point to create a cookie, since you need to
provide userid (not the e-mail) and password each time. So a
Hi Robert
Have you looked at the Download or Export option? - you get this
option, when you click on the triangle next to the names of you workflows.
Regards, Hans
On 03/27/2012 08:36 PM, Robert Chase wrote:
Hello,
We are going to migrate to a new instance of the galaxy server. Our
was hoping to be able to do something to
save the users the headache of having to export and upload their
workflows to the new server.
Regards,
-Rob
On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Robert
Have you looked at the Download or Export option
Hi Gus
Have a look at Shantanu's email from last October:
http://dev.list.galaxyproject.org/displaying-dataset-paths-in-the-UI-td4142007.html
It works very well for us.
Regards, Hans
On 04/05/2012 08:46 PM, W. Augustine Dunn III wrote:
Hello all:
There are times when I want to explore
Hi
We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').
We have encountered two issues, which I guess are related:
If I restart the server, I get:
galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
Hi Deepthi
what do you want to use the 'dynamic_options' for?
the file provided in the code tag is a pyhton script, but remember the
'code tag' is deprecated see:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccode.3E_tag_set
Regards, Hans
On 04/21/2012 12:48 AM,
at the next code update). This is
our production server.
Thank you very much for any help
Regards, Hans
On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:
Hi
We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').
We have encountered two
Galaxy installation directory (you should backup your database before
attempting this)?
$sh manage_db.sh downgrade 90
After this,
$sh manage_db.sh upgrade
Greg Von Kuster
On Apr 24, 2012, at 10:09 AM, Hans-Rudolf Hotz wrote:
Hi everybody
I usually don't like people sending the same e-mail
, I fear we will run
into problems at a later stage (ie at the next code update). This is our
production server.
Thank you very much for any help
Regards, Hans
On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:
Hi
We are in the process of migrating our Galaxy servers to the current
March 12
Hi Josh
Are you running the additional reports web site?
see: 'run_reports.sh' and 'reports_wsgi.ini'
We use this extra web site a lot for debugging. It helps tracking what
an individual user is doing - kind of 'big brother is watching you'
Regards, Hans
On 04/24/2012 10:51 PM, Dannon
Hi Deepthi
Have a look at:
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20
section: 'Variable Static Outputs determined by parameter values'
Regards, Hans
On 04/24/2012 09:29 PM, Unknown wrote:
Hi all,
Can I implement a tool which run 2 different algorithms and providing
Hi Dan
There seems to be several issues connected with each other or not, I
don't know.
- Let's start with the 'curiosity': Do you get this problem with any
tool? Does it also happen with a 'simple' (ie not using R) tool you
add?
- When you execute your R script on the command
for any help
Regards, Hans
On 04/16/2012 03:43 PM, Hans-Rudolf Hotz wrote:
Hi
We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').
We have encountered two issues, which I guess are related:
If I restart the server, I get
Hi Dan
I added this to my Rscript_wrapper.sh
script and all is well.
I am happy to hear that
and don't worry about answering my own question. There are always other
people on the list which will learn from the comments and/or find the
solution later in the mail archive ;)
regards,
Hi Ann
I am definitively interested in any form of collaboration - thank you
very much for bringing up this idea!
However, I also share some of the concerns which have been raised by
others. Even in Europe, we sometimes struggle to coordinate a conference
call with the Americas and very
On 05/03/2012 12:10 PM, Peter Cock wrote:
Hi all,
Is it possible for a Galaxy Admin to browse any user's history?
Sadly the Admin page on the wiki is still rather lean:
http://wiki.g2.bx.psu.edu/Admin/Interface
For instance, I've monitored a large Galaxy job on our cluster, and now
that it
Hi Kleo
The easiest way is to add the path information to 'run.sh', eg:
export PYTHONPATH=/data/foo/bar/python2.6/site-packages:$PYTHONPATH
(of course, you need to use a different path)
Regards, Hans
On 05/03/2012 08:29 PM, Kleo Achilleos wrote:
Dear all,
I have a local installation of
28, 2012 at 10:16 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Rob
I don't know what exactly you mean by new server. Assuming you are
just talking about different hardware:
Have you considered moving 'everything' to the new server? ie
copying the Galaxy
: the module is simply not there.
Is it working when you execute it on the the command line (as the same
user Galaxy is running as)?
Regards, Hans
Regards, Kleo.
2012/5/4 Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch
Hi Kleo
The easiest way is to add the path information
On 05/15/2012 05:42 PM, Robert Chase wrote:
Hello All,
We have a large amount of data on our production server that we would
like to make available on our new test server. I tried to move data from
our production server to our test server by copying the meta-data files
and dataset files from
Hi Marine
Could you please provide the tool definition xml file. Otherwise it is
going to be difficult to guess, what is going wrong
Regards, Hans
On 05/30/2012 11:10 AM, Marine Rohmer wrote:
Hi everyone,
I'm trying with all my best to add an NGS tool into my local Galaxy
instance.
I've
=myTool_outfile label=myTool on $o /
tests
test
/test
/tests
help
/help
/tool
/tool
there is one /tool too much
Hope this helps, Hans
Regards,
Marine
*De :* Hans-Rudolf Hotz h...@fmi.ch
*À :* Marine Rohmer
Hi Marine
If I use the xml file as you have posted in this e-mail, it works. ie it
works up to the error message:
An error occurred running this job:
/bin/sh: /home/myName/myToolRepository/bin/myTool: not found
I don't get the cheetah error you show. Are you sure, you are using the
Hi Roger
Have a look at the Reserved Variables on this wiki page:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax?#A.3Ccommand.3E_tag_set
I guess, his is what you are after?
Also, please use the 'galaxy-dev' mailing list (cc'ed) for questions
regarding local installation,
Hi
Have you looked at the wiki pages?
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently
and
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
Regards, Hans
On 06/04/2012 05:29 PM, Xu, Jianpeng wrote:
Hi,
I have installed
Hi Larry
Have you added mm10 Mouse Dec. 2011 (GRCm38/mm10) (mm10) to
~/galaxy_dist/tool-data/shared/ucsc/builds.txt
and restarted the server?
Regards, Hans
On 06/08/2012 06:19 PM, Larry Helseth wrote:
I'm trying to add mm10 to a Galaxy instance built using Mercurial on May
31st
- Please keep all replies on the list by using reply all -
check your universe_wsgi.ini file:
# Allow users to remove their datasets from disk immediately (otherwise,
# datasets will be removed after a time period specified by an
administrator in
# the cleanup scripts run via cron)
Hi Joachim
This is roughly what we did ~15 months ago:
1. make a copy of the MySQL DB (postgresdb in your case)
2. copy the complete galaxy directory to the new server (make sure you
keep the path)
3. point the new galaxy server to the DB copy and start it (different
port number)
-
Hi Peter
Have a look at Anton's talk Introduction to Galaxy at last years GCC
meeting: http://wiki.g2.bx.psu.edu/Events/GCC2011
The first few slides are talking about the history of Galaxy, eg:
Galaxy as a single Perl script (!)
Regards, Hans
On 06/12/2012 01:28 PM, Peter van Heusden
@bitsatvib
On 06/12/2012 02:29 PM, Hans-Rudolf Hotz wrote:
Hi Joachim
This is roughly what we did ~15 months ago:
1. make a copy of the MySQL DB (postgresdb in your case)
2. copy the complete galaxy directory to the new server (make sure you
keep the path)
3. point the new galaxy server
Hi Jane
I recommend mapping the data again yourself
Alternatively, you might wanna play with 'grep' (if you have the Galaxy
Unix tools installed in your Galaxy server), or use the tool 'Select
lines that match an expression'. I would do a Fastq to Tab on your data
first. Or you can try
On 06/19/2012 07:11 PM, Chebbi Mohamed Amine wrote:
Hi Galaxy team !
I'am trying to remove userless histories from my galaxy database as
mentoned in this link (
by using the command above :
python cleanup_datasets.py universe_wsgi.ini -d 60 -1
However I get an error message like this :
File
Hi Carlos
See: galaxy_dist/lib/galaxy/util/__init__.py
for characters that are allowed but need to be escaped
Regards, Hans
On 06/28/2012 03:14 PM, Carlos Reyes wrote:
Hello,
I have never used this support route before however I have a question
about a Galaxy wrapper that I made for a
Hi Jaap
are you using 'SQLite', if so, I recommend to switch to 'PostgreSQL',
see:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server/#Switching_to_a_database_server
Regards, Hans
On 07/02/2012 02:26 PM, j.w.f.van_der_heij...@lumc.nl wrote:
Hi all,
I have added
Hi Joachim
Go to Admin Menu - Security - Manage users. This will give you a list
of all users.
Alternatively, use the reports tool: Users - Date of last login and
select 0 days
Hope this helps,
Regards, Hans
On 08/06/2012 10:14 AM, Joachim Jacob wrote:
Dear devs,
How can I extract a
maybe you need to include username, password and host?
database_connection =
mysql://username:password@host/database?unix_socket=/var/run/mysqld/mysqld.sock
Regards, Hans
On 08/07/2012 03:19 AM, Kenneth Auerbach wrote:
Hello,
Galaxy runs fine 'out of the box' with the default
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