James,
I have been looking for it as well some while ago.
Would be good to post it somewhere on the wiki in a prominent place...how to
cite...
Thx
Alex
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens James Taylor
Pieter,
I just experienced the same with another generic tabular .tab file output. It
broke the filename at dash without any extension.
The file itself was ok, just the name.
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Lukasse, Pieter
Ketan,
Are workflows not the way to go for this?
We have similar tools that are usually run in sequence. We made them all
separate to allow reusing them elsewhere. For these linked tools one could
write a superscript/wrapper or design a workflow which can be public or
privately shared.
Best
Not sure if this question or solution has passed this list already but couldn't
find anything in the archive.
Is it possible to somehow insert separator lines between groups of for instance
bowtie2 indexes?
One of our tool displays it like below (the - lines); I would like to add
Peter,
We will definitely give them a try. I never understood why the tabular outputs
did have an option to include the defline/hit decription. Just for that we
needed to use the cloggy XML output and parse that into a table again.
Conserved header names are more useful to us than having column
Thomas,
Did you generate the work flow from scratch or did you make a simple analysis
in the history and extracted a work flow from that? The latter we usually do
without problems whatever...but we don't use the mothur tools though...
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
Jens,
The obvious way to temporarily solve this is by adding an additional select in
your tool xml having a low default core setting where users can select more
cores...this is however not user specific unless you let another wrapper deal
with that. This solution we use for the blast wrappers
Ricardo,
You can configure galaxy such that it will allow users to permanently delete
and purge datasets from their own histories. After deleting by pressing the
cross...select 'include deleted datasets' from the history menu. There you can
undelete but also purge immediately from disk.
So
Raj,
maybe others have a different view on this but I think just throwing you a
number is quite useless.
It all depends on YOUR data storage strategy/policy.
How long can researchers store/use their data. What are their maxed quota...Is
it backuped elsewhere, how many users. Is it public
Andreas,
export your history to tgz.
then locally import it.
I have to say that we do this for backup purposesbut it is a
pain.exporting takes sometimes ages even for small histories.
I am not sure how well synced your databases and such should be.(unique
identifiers and
+1 for me!
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: woensdag 8 mei 2013 12:06
To: Geert Vandeweyer
Cc: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re:
]
Verzonden: donderdag 28 maart 2013 15:22
Aan: Bossers, Alex
CC: Jennifer Jackson; Galaxy Dev
Onderwerp: Re: [galaxy-dev] Knowing who is currently logged into your system
Hey Alex,
Thanks for the quick response. The reason why I asked this question is because
we reimplemented our plugin WS
Akshay
If you have galaxy_reports running on your server you can see the most likely
logged in users under: Users/Date of last login when you query it for 0 days.
You at least have a login per day (not on the hour though).
For restarting purposes we ignore viewers and monitor the running jobs in
Hhhmm seems to behave normally in our running (latest) dist release
8530:a4113cc1cb5e tip
Alex
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster
Verzonden: dinsdag 12 februari 2013 12:29
Aan:
Hhhmmm.. and now it doesn't and reproduces what Joachim reported...
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: donderdag 14 februari 2013 11:45
Aan: Greg Von Kuster; joachim.ja...@vib.be
Hi All,
We are experimenting with local toolsheds for tool maintainability. On the old
galaxy wiki I can remember there was a short tutorial or small description of
the minimal requirements of a tool to be submitted to the toolshed. Actually we
submitted some.
However we seem unable to
Alex
Van: Greg Von Kuster [mailto:g...@bx.psu.edu]
Verzonden: maandag 4 februari 2013 16:25
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission
Hello Alex,
In very general terms, a repository should include everything
Ross,
Thanks! I will check it out.
Alex
Van: Ross [mailto:ross.laza...@gmail.com]
Verzonden: donderdag 20 december 2012 9:52
Aan: Bossers, Alex
CC: Samuel Lampa; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool?
Alex, xvfb http://www.xfree86
Hi
I presume the best way to optimise your current problem is to evaluate whether
you really need to groom your data!? If its old data presumably yes, but if it
is recent data in Illumina 1.8+
encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary
speedup 100% :-)
Groom
!
Alex
Van: 泽 蔡 [caizexi...@yahoo.com.cn]
Verzonden: dinsdag 4 december 2012 16:41
To: Bossers, Alex
Cc: galaxy-dev@lists.bx.psu.edu
Onderwerp: 回复： [galaxy-dev] 回复： Speed up the galaxy
Hi Alex
I look the page of wikipedia, but I have a little confused. We sequenced
instance into a fresh onebut failed due to all
sorts of unpredictable errors..
Alex
-Oorspronkelijk bericht-
Van: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Verzonden: donderdag 29 november 2012 17:35
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu Galaxy-dev
Onderwerp: Re
Philippe,
As far as I know most of the styling is in
galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present
in that location.
Changes might only be visible when restarting the instance though!
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
Dear all,
Would it be possible somehow to not only export a single history of a user (to
file) but also all histories of a user in one go. Or even all user-bound
histories/settings and such?
I would like to import them into another galaxy instance (basically from our
internal development
Andreas,
I am not sure if you can call these surprises.
Some tools (which I highly appreciate) of Peter have been parallelised to get
the job done more quickly. I earlier mentioned the ncbi blast+ wrappers but
there the tool by itself handles the multithreading.
Other tools I am aware that use a
Andreas,
Yes this is possible. You can also have a look at the ncbi blast+ tools written
by Peter. The same is true.
Usually the tool wrappers (xml) have an option preconfigured how many threads
can be used... You can adjust these directly in the xml OR as we did we added
the option to be
Dannon,
I wanted to apply the patch as well on our fresh instance. But it fails with
the error of uncomitted changes..
But we only pull/merge/update using hg nothing else we do with itany clues?
We only locally modified files of course (like the wsgi.ini files and loc
files).
$ hg patch
if it solves issues or upgrades better
Alex
-Oorspronkelijk bericht-
Van: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Verzonden: dinsdag 13 november 2012 14:16
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Errors in creating galaxy DB in MySQL for fresh
galaxy
...@bx.psu.edu]
Verzonden: dinsdag 13 november 2012 16:45
Aan: Bossers, Alex
CC: Galaxy Dev List
Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist
On Nov 12, 2012, at 2:43 PM, Nate Coraor wrote:
On Nov 12, 2012, at 2:35 PM, Bossers, Alex wrote:
Nate,
crapthat fixed
-Oorspronkelijk bericht-
Van: Nate Coraor [mailto:n...@bx.psu.edu]
Verzonden: dinsdag 13 november 2012 16:45
Aan: Bossers, Alex
CC: Galaxy Dev List
Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist
On Nov 12, 2012, at 2:43 PM, Nate Coraor wrote:
On Nov 12, 2012, at 2:35 PM, Bossers
Dear all,
I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems
to work fine.
However in the admin panel when I make a quotum it works unless I let it make
default at the same time or allocate groups of users to the quota.
Just creating the quotem works fine without any
Hi All,
Due to previous DB errors we decided to let galaxy-dist repopulate the database
(MySQL). We purged all tables from the DB and when restarting galaxy it
repopulates the DB on the fly while doing all migration steps. A nicely running
galaxy as the result.
I encountered a strange error
...@bx.psu.edu]
Verzonden: maandag 12 november 2012 20:03
To: Bossers, Alex
Cc: Galaxy Dev List
Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist
On Nov 12, 2012, at 5:38 AM, Bossers, Alex wrote:
Dear all,
I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems
Some additional info;
Actually the errors already started at migrate version 93-94.
I just restored the version to prior upgrade to check any other errors. There
were some create errors. I am not sure if these come from the \n\t statements
in the sysntax or whether that is just an error log
After a fresh galaxy-dist pull today (no update for various reasons) the
instance was running ok on the default sqlight database.
When I migrated back the setting to use the MySQL database it complained during
startup about having found an old version of the database and I need to upgrade.
Dear all,
I might have missed it on the list and cannot find it in the archive;
When we import a history exported from the same or another galaxy instance it
imports ok and all files are there and usuable, only the history size is 0.
We are up to latest galaxy-central of October 4th.
Is this a
Another problem;
On our ubuntu x64 server with the latest galaxy_central of Oct 4th...
An export of the history sized 2.5Gb was ok. However large exports (like 10Gb)
make the server instantly crash (within a few seconds) without anything
significant in the galaxy.log.
The apache server is still
Hi All,
Maybe I missed it on the list here, but it seems that for samtools the pileup
command has been deprecated without backward compatibility from the more recent
samtools packages...
http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html
Did anyone rewrite some of the
pileup command
cmd = 'samtools mpileup %s -f %s %s %s'
try:
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: vrijdag 20 juli 2012 12:20
Aan: 'galaxy-dev@lists.bx.psu.edu'
Onderwerp: [galaxy-dev] samtools pileup
Joachim,
If I remember correctly for our galaxy proftpd setup on ubuntu 10.10.
Be sure to compile proftpd with the required additional SQL modules.
Then figure out the user and group ids of galaxy user that can access the DB
(mysql in our case).
$ id galaxy (or whatever user you use)
Make sure
You mean the javascript works right? Or did you manage to get the PHP inside?
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Smithies, Russell
Verzonden: donderdag 14 juni 2012 1:45
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev]
You can do so / allowing them to, by using the galaxy ftp solution.
That way users can link or provide files in their email subdirs. You have to
sort out how to set the users/rights properly on your linux box though.
But see the galaxy ftp solution pages, it might be of help.
Alex
As an alternative you can return hidden history items.
Not exactly what you want perhaps...
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: maandag 2 april 2012 15:38
and not complaining. Is there any way to
verify uploads are processed through nginx?
jorrit
On 03/05/2012 08:37 PM, Nate Coraor wrote:
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
Early 2011 there was a discussion and feature request to be able to refresh loc
files on a running galaxy instance.
This is not only convenient for updating loc files for blast, bowtie, bwa and
such, but also opens possibilities to update and dynamically populate such
files to be used in other
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 (10Mb+ tarballs) AND large files! Furthermore its seems
to be in FireFox only They upload fine using IE8 or 9. Didn't test other
browsers though.
Ok. Just filed a bug report.
Alex
-Oorspronkelijk bericht-
Van: Langhorst, Brad [mailto:langho...@neb.com]
Verzonden: maandag 13 februari 2012 17:38
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] history box odd behaviour
On Feb 13, 2012, at 11:22 AM
PS: when I make the section empty again in the original tool_conf.xml it
doesn't show up anymore in that section. :-(
Actually the complete section is again invisible.
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: maandag 6
tested it with an empty section AND an empty shed_tool_conf
thoughwill try to later...when I figured out how to completely remove a
tool from the system.
Thanks for the quick fix!
Alex
Van: Greg Von Kuster [mailto:g...@bx.psu.edu]
Verzonden: maandag 6 februari 2012 16:21
Aan: Bossers, Alex
CC
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs.
Now I am able to get tools from the galaxy main toolshed. Tested the table2html
tool to be sure about no additional dependencies. It came up nicely with the
section list I can install a tool to; but...
I created an
Somehow I seem to miss something when configuring our latest up-to-date
galaxy_central version to use the galaxy toolshed.
When as admin I want to install a tool I can browse the given 2 repositories
and select view tools.
When I select install to local galaxy it drops an error on 2 tools I
PS: This only seems to be true when disk quotas are in place. So where to
get the per user disk usage?
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: maandag 30 januari 2012 8:56
Aan
: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] How to delete user (and unshared files) in local
instance by galaxy-admin (panel)
On Jan 27, 2012, at 4:43 PM, Bossers, Alex wrote:
Hi All,
We are finally up-and-running again with the latest dist release
Greg,
Thanks. Stupid to have missed that universe setting
Alex
Van: Greg Von Kuster [mailto:g...@bx.psu.edu]
Verzonden: zaterdag 28 januari 2012 16:26
Aan: Bossers, Alex
CC: Hans-Rudolf Hotz; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] How to delete user (and unshared files
Reading this on the wiki: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas
Shows that there is a record in the DB tracking the users allocated diskspace
for histories.
Is there a convenient way to get this info using the galaxy admin panels?
Thereby we can track heavy users and urge them to
Van: Hans-Rudolf Hotz [h...@fmi.ch]
Verzonden: zaterdag 28 januari 2012 13:10
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] How to delete user (and unshared files) in local
instance by galaxy-admin (panel)
Hi Alex
Since
Hi All,
We are finally up-and-running again with the latest dist release. The previoous
version was ok but already quite old.
For our local public server at wur we are now encountering the awaited disk
space issues. as had to come some daybut sooner anyway... So we have
been cleaning
Dan,
any idea when the next dist release is scheduled? We need to upgrade our wur
instance seriously and from then keep up the pace, but it would be a pity if we
upgrade and extensively test it now, while the new release is out a few days
later.
The latest is from November 18th right?!
Thanks
@lists.bx.psu.edu; Bossers, Alex
Onderwerp: re: Hidden history item
Alex,
I just implemented this functionality in galaxy-central changset 303741fda0ec
and documented it on the wiki.
https://bitbucket.org/galaxy/galaxy-central/changeset/303741fda0ec
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config
+1 for me :-)
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Casey Bergman [casey.berg...@manchester.ac.uk]
Verzonden: donderdag 15 december 2011 20:10
Aan: Peter Cock; Sean Davis
CC: galaxy-dev@lists.bx.psu.edu
Hi
The fasta-manipulation section on toolshed seems to be down
(http://toolshed.g2.bx.psu.edu/). Am I the only one experiencing this?
IE just returns me a blank error page not found. FF returns me another
unhelpful error:
Server Error
An error occurred. See the error logs for
The blast+ wrappers have DUST capability ON by default
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Smithies, Russell
Verzonden: maandag 28 november 2011 1:27
Aan: 'Björn Grüning'
CC:
Shaun,
we took this quite easily by a simple tool we added to the toolbox. Just use
the xml below as a new tool and you can get file paths of any file you like.
Hope it helps,
Alex
tool id=filelocator name=Locate Data in Galaxy Database version=1.0.1
description/description
commandecho
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 selecting the view_deleted
, Alex
CC: 'galaxy-dev@lists.bx.psu.edu'
Onderwerp: RE: filter
Hi thanks, but what sanitizer option should I set it to?
-Original Message-
From: Bossers, Alex [mailto:alex.boss...@wur.nl]
Sent: Thursday, August 04, 2011 3:11 PM
To: KOH Jia Yu Jayce
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject
You can also directly link the R script in the galaxy-tool.
We have many of those. For testing (NOT SAFE!) we also have a tool that allows
the upload of an R script for testing purposes
See the arhives for more extensive discussion...
command
R --slave --vanilla
On our up-to-date galaxy_central version I have successfully moved the
database/files directory to mounted storage. After adapting the
universe_wsgi.ini it works fine after galaxy restart.
Now the tool-data dir becomes bigger and bigger and I wanted to move that to
mounted storage as well.
I
Mus_musculus.NCBIM37Mus musculus NCBIM37
/share/bowtie/indexes/Mus_musculus.NCBIM37 Mouse
--
-Oorspronkelijk bericht-
Van: Ross [mailto:ross.laza...@gmail.com]
Verzonden: vrijdag 22 juli 2011 15:15
Aan: Bossers, Alex
Onderwerp: Re: [galaxy-dev] Error moving tool-data dir
Hi all,
by default I let my tools produce (the old way) a logfile of the console and
additional running statistics. This is convenient at tool setup and
ocassionally for troubleshooting. Anyway I would like to make the corresponding
history item hidden. I tried including hidden=true in the
In our local instance (central version) up to changeset (June 28th) I noticed
in the admin panel to manage jobs some odd behaviour;
When I set the update Jobs cutoff on 10 seconds and press refresh the item
below (administrative Job Lock) is also activated and new jobs are locked.
Is that a
Paul,
as far as I know the config files (probably loc files) are only refreshed on
galaxy_instance restart unfortunatly.
So when this is possible to do on the fly I am interested as well.
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
Our first tools arrived at the toolshed; The MUMmer genome comparison suite and
a TopHit filter.
Enjoy and we appreciate any feedback for improvement:
http://community.g2.bx.psu.edu/tool/browse_tools?operation=tools_by_categoryid=062d90505b2e763dwebapp=community
Alex
Peter,
if you were just interested in having a dynamic refresh it was posted long
time ago and we have it operational. It comes as a tool in your tool list and
refreshes all from the tool_conf.xml. Not the loc filtes though! As far as i
remember it doesn't kill running jobs.
It requires two
Alternatively you can redirect your STDOUT and/or STDERR into a LOG txt file as
additional output to the tool.
I do many times the same since it allows the realtime tracking in the log file
of the process where it is and when it's expected to be finished.
Indeed a wrapper can be used but if you
PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT
and STDOUT to a logfile. You won't get a red box though when errors occur!
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: donderdag 26 mei 2011 15
, Alex
CC: shashi shekhar; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] stdout and stderr
On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote:
PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT
and STDOUT to a logfile. You won’t get a red box
Ah right. Overlooked the shortcut EMPTY
Just not my way of doing it..
Alex
Van: Vipin TS [vipin...@gmail.com]
Verzonden: maandag 23 mei 2011 17:39
Aan: Bossers, Alex
CC: Jayant Khopale; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Need help
Hello all,
Maybe I posted it wrong. But below my original message again.
Any ideas?
Thanks
Alex
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: zaterdag 19 maart 2011 10:23
Aan: galaxy-dev
Hi All,
I have some tools that generate some tabular output. The next step is to
aggregate the data for some filtering and analysis. In my view the best way to
do by using a DB (MySQL in my case).
Tools and cmd line wrappers can easily connect to this DB (another database
than galaxy is using
Branden,
we have also customised the tol menu and added a university specific section on
top just beneath Get data.
We have also listed tools twice for convenience. I do not see the need t list a
tool twice in the same expanding section. But in another section it should work
flawlessly.
Having
Hello all,
I have a tool based on blastdbcmd that contains a param tag of type text. I
want to be able to use the % sign in that text field users can enter (%g is for
instance the field identifier for gi). However, if I do for instance %f or %f
it returns Xf or Xf in the the variable.
For
Hello all,
I have a tool based on blastdbcmd that contains a param tag of type text. I
want to be able to use the % sign in that text field users can enter (%g is for
instance the field identifier for gi). However, if I do for instance %f or %f
it returns Xf or Xf in the the variable.
For
...@gmail.com]
Verzonden: woensdag 16 februari 2011 15:44
Aan: Bossers, Alex
CC: galaxy-...@bx.psu.edu
Onderwerp: Re: [galaxy-dev] Percent and pipe sign in text input fields
Hi Alex,
Galaxy sanitizes the params to remove unsafe characters. It's a security
feature. From a previous post some time
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