Hi all,
I'm aware that in an individual tool's XML wrapper you can add
hidden=true to the tool element to hide the tool from the
listing shown in Galaxy's left hand panel (but the tool is still
loaded and can be called by old workflows etc).
Can this be done via the tool_conf.xml file as well?
On Fri, Feb 18, 2011 at 5:01 PM, Ryan Golhar golha...@umdnj.edu wrote:
Ok, I don't know what happened with this...I reinstalled from scratch and ...
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py, line
16, in ?
...
File
On Thu, Feb 10, 2011 at 5:58 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm aware that in an individual tool's XML wrapper you can add
hidden=true to the tool element to hide the tool from the
listing shown in Galaxy's left hand panel (but the tool is still
loaded and can
Hi all,
I have a multi-step workflow where I've marked some parameters to be
set at run time (in this case, a minimum read length, used in two
different workflow steps). I want to use the same parameter value in
multiple tools, rather than give the user one prompt for each tool. Is
this possible?
On Wed, Mar 2, 2011 at 3:42 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
P.S. I do like the color highlighting and live substitution of
the workflow parameters into each tool step that uses them.
Very slick!
That was the good news. Now the bad news - two bug reports.
Firstly if you clear
Hi all,
Is there any documentation on what Galaxy means by the different qual formats?
In particular why is there a qual454 and not a qualsanger (to match fastq)?
Historically QUAL files were used back in Sanger/capillary sequencing
by PHRED, and just hold PHRED scores as integers. This was
:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock,
Erwin Frise, Darin London, Ron Taylor
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http://lists.open-bio.org/mailman/listinfo/bosc
On Sun, Mar 6, 2011 at 6:36 AM, Zhi-Wei Lu z...@ucdavis.edu wrote:
Hi Galaxy developers,
I have download the galaxy code via mercurial
hg clone https://bitbucket.org/galaxy/galaxy-central
The downloaded code, however, does not contain the setup.sh file.
Could you let me know how do I run
On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote:
Ryan Golhar wrote:
I have a local instance running. When I'm logged in as user1, log
out, then try to log in as user2, I keep getting the You have been
logged out message.
Its as if the browser's cache is retaining some
On Thu, Mar 10, 2011 at 5:53 PM, Glen Beane glen.be...@jax.org wrote:
On Mar 10, 2011, at 12:24 PM, Peter Cock wrote:
Hi all,
Via the Galaxy admin interface, I'm currently importing some BAM
files into a library from the local file system. Since they are big, I
don't want Galaxy to copy
On Fri, Mar 11, 2011 at 3:04 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
Thanks for the patch - I've applied a corrected version of it in change
set 5215:74c4dd43485a. Let me know if you'd rather have me flip
the Copy data into Galaxy? feature. I'd be happy to, but I don't
Hi all,
I've been exploring how to use Galaxy's shared library functionality,
and have noticed that once imported into a working history, that the
little 'i' information icon's black popup window isn't working for these
datasets. All it says is 'Could not find the job for this dataset.'
This
On Fri, Mar 18, 2011 at 6:12 PM, Kanwei Li kan...@gmail.com wrote:
Thanks for reporting, committed fix
https://bitbucket.org/galaxy/galaxy-central/changeset/3070455afbdd
Thanks,
Peter
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On Tue, Mar 29, 2011 at 1:31 AM, Assaf Gordon gor...@cshl.edu wrote:
Hello all,
We're developing alternative bowtie tools that more closely suit our
needs, are we're happy to share (and get comments).
The main differences are:
1. separate tools for paired-end and single-end
Sounds sensible
On Tue, Mar 29, 2011 at 4:46 PM, Assaf Gordon gor...@cshl.edu wrote:
Hi Dan,
Daniel Blankenberg wrote, On 03/29/2011 10:55 AM:
When files are added to Galaxy, the datatype can be directly set to
any of the fastq variants (e.g. fastqillumina), which removes the
requirement of grooming (but
Hi all,
The NCBI have just released BLAST 2.2.25+ which includes some
interesting new stuff of interest to the tabular output, i.e.
Added support for query and subject length to tabular output
I would therefore like to update my BLAST+ wrappers in Galaxy to add
these two columns to the
On Fri, Apr 1, 2011 at 3:55 PM, Kanwei Li kan...@gmail.com wrote:
Hi Peter,
I don't see your attempt to use default in the example given. A bit more
detail?
-K
Hi Kanwei,
My example tool is now here:
https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30
As per the original
On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi all,
The NCBI have just released BLAST 2.2.25+ which
On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li kan...@gmail.com wrote:
I tried both ways, no dice (you can try yourself with a clean
galaxy-central base)
I'm a bit puzzled and not an hg expert. Was there an error message?
And for plan (B), what went wrong with using patch and the raw
changes?
On Mon, Apr 4, 2011 at 4:36 PM, Kanwei Li kan...@gmail.com wrote:
dhcp243253:galaxy-central kanwei$ hg transplant -s
~/peter/galaxy-central/ -b blast25
searching for changes
changeset: 5585:ab40f95393ec
branch: blast25
parent: 5583:086c9c2c52b9
user: peterjc
On Tue, Apr 5, 2011 at 10:58 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'd like to write a tool test where the sample output and the
generated output are the same except for white space.
i.e. running diff with the -w switch reports no differences.
Is this possible
On Mon, Apr 4, 2011 at 6:07 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li kan...@gmail.com wrote:
Done the manual way
Thanks.
I was hoping to have finished this today, but it turns out there are
some subtle but annoying changes to how BLAST
Hi all,
I had wondered why none of the tools on the Galaxy Tool Shed had a
rating, and had assumed it was just that so far no-one had bothered. I
have a new theory, it doesn't work?
I just viewed Brad's BAM to BigWig tool, clicked on Tool Actions
then Rate Tool, and got:
Server Error
An error
On Wed, Apr 6, 2011 at 12:44 AM, Zhe Chen z...@lanl.gov wrote:
Hi,
My tool has a script reads a file in the same directory as the script.
When I try to use relative path to read the file, it works by directly run
it, but does not work when calling from Galaxy. Absolute path will work,
but I
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar golha...@umdnj.edu wrote:
I just updated my local galaxy instance using hg pull, and the history items
are no longer expandable. What happened?
Which browser(s) are affected? I recall reporting some issues
with Internet Explorer only and the history
On Thu, Apr 14, 2011 at 2:08 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi,
I have a tool with a code file=my_script.py/ tag and in that code file
I'm trying to get the tool dirpath where that script and the tool XML
exist. I've tried:
Hi all,
I just wanted to mention (to avoid duplicate work) that I have a working
Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear
localization signals (NLSs) from a protein FASTA file. The wrapper
does a little reformatting of the output to get a clean tabular file for use
in
On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
For standard Python tools in Galaxy, I'm using
os.path.split(sys.argv[0])[0]
to get the path, which on reflection probably should
Hi all,
I'm working on a tool where the repeat tag looks like an elegant
solution - however I want to limit the number of repeats to be 1, 2 or 3.
i.e. I want to set min=1 and max=3 attributes for the repeat,
based on analogy to the param tag.
Is this possible, but not documented here?
On Tue, Apr 19, 2011 at 1:46 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
Yes, setting min and max values in the repeat tag should work as you need.
As you point out, it is probably not well documented, so please let us know
if it isn't working as you imagine it should.
Thanks
Hi Kanwei,
I noticed that the BLAST+ output options for HTML are not working,
a side effect of my recent refactoring. Could you transplant/merge this
fix and test please:
https://bitbucket.org/peterjc/galaxy-central/changeset/e1e6f92e07bf
Hi all,
I'm working on a simple plotting tool, and currently I am using PDF
output since this is vector based (so it can be rescaled without loss
of quality) and can be edited easily enough for use in publications.
However, at least on my OS/Browser, Galaxy does not show the
PDF files in situ,
On Wed, Apr 20, 2011 at 10:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm working on a simple plotting tool, and currently I am using PDF
output since this is vector based (so it can be rescaled without loss
of quality) and can be edited easily enough for use in publications
On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx
pieter.neeri...@gmail.com wrote:
Hi Peter,
On Apr 20, 2011, at 11:07 AM, Peter Cock wrote:
Hi all,
...cut...
How about SVG? Don't most of the mainline browsers have
reasonably good SVG support built in (possibly via a plugin)?
Yep, SVG
On Thu, Apr 21, 2011 at 10:50 AM, Pieter Neerincx
pieter.neeri...@gmail.com wrote:
Hi Peter,
On Apr 20, 2011, at 5:47 PM, Peter Cock wrote:
On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx
pieter.neeri...@gmail.com wrote:
Hi Peter,
On Apr 20, 2011, at 11:07 AM, Peter Cock wrote:
Hi all
Hi all,
Our Galaxy is running on a shared server which will sometimes be running
other computationally demanding jobs (outside of Galaxy). In some cases
I'd like these to have priority, perhaps by having Galaxy run the tool child
processes at a nice level of 10 (say).
Is there any built in way
On Thu, Apr 21, 2011 at 5:43 PM, Assaf Gordon gor...@cshl.edu wrote:
Hi Peter,
Peter Cock wrote, On 04/21/2011 11:00 AM:
Is there any built in way to control the Unix priority level (e.g.
nice or ionice) used to run tasks? I don't see anything on here,
but perhaps I'm looking in the wrong
2011/4/22 liyanhui607 liyanhui...@163.com:
Dear Sir,
We have a program writen in C lanuage. It can run nomally in linux
environment.
We plan to add it to galaxy, but it did not work.
The C file after complie named shortest-path
The
2011/4/25 liyanhui607 liyanhui...@163.com:
Thank you very much!
After I have added it to the path, it can work now.
Best Wishes!
Yan-Hui Li
Oh good.
Peter
P.S. Please keep the mailing list on replies.
___
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Hi all,
So far we've been running our local Galaxy instance on
a single machine, but I would like to be able to offload
(some) jobs onto our local SGE cluster. I've been reading
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
Unfortunately in our setup the SGE cluster head node
On Tue, Apr 26, 2011 at 12:10 PM, Sean Davis sdav...@mail.nih.gov wrote:
On Tue, Apr 26, 2011 at 5:11 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
So far we've been running our local Galaxy instance on
a single machine, but I would like to be able to offload
(some) jobs onto our
Hi all,
I mentioned just over a month ago that I had written a Galaxy tool
to do find Reciprocal Best Hits (RBH) from BLAST tabular output
or similar (e.g. Bill Pearson's FASTA tabular output).
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html
On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Ed
You can use the variable $userEmail in the 'command' tag of the tool
definition file
Regards, Hans
That should probably be listed on the wiki,
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Are
On Fri, May 6, 2011 at 10:17 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote:
Hi, I have created a tool that will fetch sequences for selected IDs from a
tabular file containing multiple IDs and additional info.
I want the tool config to scan the first column of the tab file for IDs and
On Saturday, May 7, 2011, drho...@uark.edu wrote:
Thanks Peter, I debated which to post to.
This is just using the Megablast tool in Galaxy. My IT people are not
Biologists. They had
this working fine and some tweak has screwed up the GI column in the results
file. It should
be the
Hi all,
To make someone an administrator on a local Galaxy install, do I just
need to add their email (login) to the comma separated setting
admin_users in universe_wsgi.ini?
https://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface
I have this working on one server, but it doesn't
On Mon, May 9, 2011 at 12:48 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Peter
First,the obvious question: Have you restarted galaxy?
Yes, and I tried hard reloads in two different browsers (both of which
are working on the primary server).
Second: I vaguely remember a similar problem, and if
On Thu, May 12, 2011 at 6:03 PM, Leandro Hermida wrote:
Hi, how do you make float parameter types fully optional? optional=true
doesn't work.
-Leandro
Sadly this is a known bug I reported some time ago:
https://bitbucket.org/galaxy/galaxy-central/issue/403
Peter
On Wed, Apr 6, 2011 at 10:30 PM, Luobin Yang yangl...@isu.edu wrote:
Hi,
The reload a tool's configuration menu avoids restarting Galaxy system
when a tool's web interface changed, but it doesn't seem to reload the
.loc files that a tool's XML file uses. I am wondering if it's possible to
On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros j.f.j.la...@lumc.nl wrote:
Hi Pieter,
Thanks for the reply, but from the looks of it, this is a way to incorporate
webservice clients into galaxy. What I want is slightly different.
I'm talking about adding a normal command line tool (an
Hi all,
I'm wondering if the following task can be done in Galaxy with the
standard tools. The specific example is selecting the top (e.g. 3)
match sequences for each blast query, but I see this problem as much
more general than a Select top BLAST hits tool.
I want to select the first few (e.g.
Hi all,
I recently started trying out the Share workflow functionality on
our local Galaxy, so that I could make available some general interest
workflows to all our users, rather than sharing them with individuals
one by one. However, once published, it was not easy to find them! I
eventually
On Wed, May 18, 2011 at 3:54 AM, Kanwei Li kan...@gmail.com wrote:
Hi Peter,
I think the tool shed would be appropriate for this...
-K
OK - I'll do that.
Thanks,
Peter
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On Tue, May 17, 2011 at 5:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm wondering if the following task can be done in Galaxy with the
standard tools. The specific example is selecting the top (e.g. 3)
match sequences for each blast query, but I see this problem as much
more
On Thu, May 19, 2011 at 7:33 PM, madduri gal...@ci.uchicago.edu wrote:
I wonder if somebody can give me more context around this issue..
On 3rd May I emailed IBX about their Galaxy install and one of
the (in house) tools mentioned on the workflow image here:
2011/5/20 Louise-Amélie Schmitt louise-amelie.schm...@embl.de:
Well I'm still missing something...
Is there a way to use the conditional tag sets in the tool's xml with it? To
suppress the unnecessary options for a given file type? or more than one?
It sounds like you want to use the
On Mon, May 16, 2011 at 8:59 PM, Spunde, Alex aspu...@illumina.com wrote:
Same thing:
[aspunde@ilmnhw-biolin10 galaxy-dist]$ python ./scripts/fetch_eggs.py
Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
Fetched
On Mon, May 23, 2011 at 3:09 PM, Anton Nekrutenko an...@bx.psu.edu wrote:
Dear Peter:
Yes, that would help.
One possibility would be to have all new bugs CC'd to the dev
mailing list? Not sure if everyone here would like that or not...
But, you patches are definitely not unnoticed. We'll
On Tue, May 24, 2011 at 3:12 PM, Johannes Eichner
johannes.eich...@uni-tuebingen.de wrote:
Dear Galaxy-Dev Team,
is it possible to display the headers of the columns which can be
selected in a data_column parameter? Currently, only the column index
(e.g., c1, c2, etc.) is displayed in Galaxy.
On Wed, May 18, 2011 at 6:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Kanwei,
Could you merge this branch or transplant this fix please?
https://bitbucket.org/peterjc/galaxy-central/changeset/3c0b903c86a9
https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_05_18
New
On Wed, May 25, 2011 at 1:10 PM, Kanwei Li kan...@gmail.com wrote:
Sorry, it slipped by. Committed!
No problem - thank you,
Peter
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On Thu, May 26, 2011 at 10:34 AM, Roman Valls brainst...@nopcode.org wrote:
Nate, is it just me or all the .png links on that wikipage are
broken/missing ? :-S
I've noticed this on other pages, I think some stuff got moved a while back.
They just need the folder name prefixed...
Peter
On Thu, May 26, 2011 at 1:36 PM, shashi shekhar meshash...@gmail.com wrote:
Hi all,
I am using one tool which gives stdout and stderr . it is showing red color
(job failed) in browser.How can i resolve such type of problem.
Regards
shashi shekhar
See issue 325,
On Thu, May 26, 2011 at 1:22 PM, Kempenaar, M (med)
m.kempen...@med.umcg.nl wrote:
Hi list,
I've been working on a single Galaxy tool for a while now, and I'm running
into all sorts of difficulties that can probably all be fixed using Cheetah.
However I've been trying several ways of utilizing
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 though when errors occur!
Right - if you need to detect an error state via the return code,
On Thu, May 26, 2011 at 3:45 PM, Johannes Eichner
johannes.eich...@uni-tuebingen.de wrote:
Hi Peter,
I defined an additional metadata element for the column names
analogously to the column_types element in the module
galaxy_basedir/lib/galaxy/tools/datatypes/tabular.py:
MetadataElement(
On Mon, May 23, 2011 at 3:34 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, May 23, 2011 at 3:09 PM, Anton Nekrutenko an...@bx.psu.edu wrote:
Dear Peter:
Yes, that would help.
One possibility would be to have all new bugs CC'd to the dev
mailing list? Not sure if everyone here
On Fri, May 27, 2011 at 11:21 AM, Vossen, Bodo
bodo.vos...@mpi-bn.mpg.de wrote:
Hi all,
I've implemented functionality for adding tools via the admin menu.
That sounds very useful in principle, although perhaps
the less flexible alternative of reloading tool_conf.xml
would achieve the same
On Mon, May 30, 2011 at 10:42 PM, Bossers, Alex wrote:
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.
I'd like to see something like this
Dear all,
I was thinking about how to improve some of my tools and
wondered if there is any way to have dynamic default values
for parameters (depending on other parameters).
Obviously this won't make sense in all cases, but as a specific
example, consider my Venn Diagram tool:
On Wed, Jun 1, 2011 at 3:22 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Peter,
Greg will probably reply, but I'll throw in my $0.02 as well.
Great - but with your answers you've triggered more questions ;)
Peter Cock wrote:
Hi Greg et al,
I've just been looking over your slides from last
On Wed, Jun 1, 2011 at 4:22 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter - I finally got a chance to jump in - see my inline comments...
Hi :)
What happens with branches? Would the Tool Shed just show the
default branch? That seems best for a simple UI.
Some of the branching
On Wed, Jun 1, 2011 at 5:25 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
Well, yes and no - as long as there are competing versions of a Galaxy tool
(e.g. from an original author and a fork by a second author), and they use
the same ID in their XML, you have a clash
On Tue, May 31, 2011 at 11:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
As I mentioned on Twitter, at the end of last week I wrapped Blast2GO
for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See
http://blast2go.org/
Currently current code is on bitbucket under
Hi all,
I have a couple of minor suggestions for improving the website
http://galaxy.psu.edu/gcc2011/Home.html
First, please fill in a meaningful HTML titles since that will be used
as the default caption in a bookmark, tab or window title.
Second, please add a link to the presentation slides
On Wed, Oct 6, 2010 at 11:16 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Tue, Sep 28, 2010 at 12:04 PM, Peter pe...@maubp.freeserve.co.uk wrote:
Hi all,
I'm wondering if there is any established way to share parameter
definitions between tool wrapper XML files?
For example, I am
Hi all,
Something I've not needed to do until now is define a new file format
in Galaxy. I understand the basic principle and defining a subclass in
Python... however, how does this work with new tools on the Tool Shed?
In particular, if an output format is likely to be used by more than
one
On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster g...@bx.psu.edu wrote:
We will certainly include support for new data formats into the Galaxy core.
In case you haven't seen it, details for adding new formats is available in
our wiki at
On Mon, Jun 6, 2011 at 2:45 PM, Mariette jmari...@toulouse.inra.fr wrote:
Hi everyone,
I'm new in galaxy and I want to create a component, so I have multiple
questions.
The component executes a script which takes different formats :
fasta|fastq|sff. As output it takes a folder, to do so I
On Mon, Jun 6, 2011 at 11:18 AM, James Taylor ja...@jamestaylor.org wrote:
Peter, most of the current UI theme was designed by someone who is
red-green colorblind (me), and we avoid using color alone for encoding
information. The change has been reverted, thanks for brining it to our
On Tue, Jun 7, 2011 at 9:24 AM, Mariette jmari...@toulouse.inra.fr wrote:
Thanks for the answer,
so I tryed to write a wrapper, but the main script is not recognize.
When I'm calling my wrapper in the xml file, I don't have to specify
the full path but then from my wrapper if I want to call
On Tue, Jun 7, 2011 at 10:56 AM, Mariette jmari...@toulouse.inra.fr wrote:
Thanks for the answer,
Still considering the number of outputed files problem. In my script I know
that if
a cleaning option is set 2 other files will be created, so I check if the
option is asked by the
user and try
On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnson johns...@umn.edu wrote:
I added an attribute format_source (analogous to metadata_source)
to the data tag to deal with that kind of issue:
see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Where is the code to handle this?
On Tue, May 17, 2011 at 2:21 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
That sounds really useful - it is something that you plan on adding
to Galaxy officially?
Yes, I'm working on adding a lot of user- and admin- side access to
various numbers about disk usage (used
On Wed, Jun 15, 2011 at 2:30 AM, Ka Ming Nip km...@bcgsc.ca wrote:
Hello,
I have been trying to set up Galaxy to run its jobs on my SGE
cluster using the Unified Method, based on the steps described
in the wiki:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
My local
On Thu, Jun 9, 2011 at 4:20 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
Hi Nate,
Since you're looking at this kind of thing, would the Saved Histories
page be worth updating to show the size on disk of each history? As
a Galaxy user that seems moderately useful - although
On Thu, Jun 16, 2011 at 3:00 AM, Ravi Madduri madd...@mcs.anl.gov wrote:
I apologize for jumping on to this thread a bit late. I read below that
there is a plan to pull tools into a galaxy installation automagically. I
wonder if you plan on providing some kind of API to query the tool registry
Hi all,
I just tried updating one of my tools on the new hg based Galaxy Tool
Shed and ran into some issues. I guess I'm the first person to try
this...
First of all, there is no clear update action like there used to me.
Could that be restored please?
On Thu, Jun 16, 2011 at 2:23 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
If you were curious it was fixed about 7 hours later in 5681:0886ed0a8c9f
Thanks for using Galaxy,
Dan
Thanks - I know this kind of unexpected breakage is inevitable sometimes,
but would recommend tool
On Thu, Jun 16, 2011 at 3:01 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
Production servers, or any server where you have users, should always track
Galaxy-dist.
Yes, that's very clear.
Galaxy-central is a development repo (you get access to the latest and
greatest, but also
On Thu, Jun 16, 2011 at 3:26 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
I understand, and that is why I am working feverishly to add features
that do not force the use of hg form the command line (I've got several
features functional, but not everything yet). The current tool shed
On Thu, Jun 16, 2011 at 4:31 PM, Robert Jackson rj...@utpa.edu wrote:
Does anyone have practical information for installation and set up for the
galaxy distribution on a cluster??
Did you not get these replies?
http://lists.bx.psu.edu/pipermail/galaxy-user/2011-June/002715.html
On Thu, Jun 16, 2011 at 5:40 PM, Chris Fields cjfie...@illinois.edu wrote:
I'm of the opposite mind; I'm not sure there is an absolute need to
have one's tools be a branch or fork of the main tool shed, though
I agree there is also utility in allowing that (having a customized
'main' repo, or
On Tue, Jun 28, 2011 at 9:52 PM, George Michopoulos
gior...@stanford.edu wrote:
Hey everyone,
Hope all is well! I was wondering if someone could help me with
another error I ran into. I recently downloaded the NCBI BLAST+ toolkit and
it automatically installed itself into Galaxy. I'm just
On Thu, Jun 30, 2011 at 1:26 AM, George Yianni Michopoulos wrote:
Hey Peter,
Thanks so much for your help, your comments helped me realize what
was wrong. The issue was that I wasn't including the name of the
database within the path, just the folder it was in!
Best,
George Michopoulos
On Mon, Jul 4, 2011 at 1:46 PM, Sarah Diehl di...@immunbio.mpg.de wrote:
Hello,
in the config of a tool I want to integrate into Galaxy I would like to have
a parameter with the following properties:
param name=var type=integer label=Var value=50 optional=true
min=10 max=100 /
So it
On Tue, Jul 5, 2011 at 7:24 PM, Greg Von Kuster g...@bx.psu.edu wrote:
I have previously commented on the problem with showing the
description on its own without the context of the tool name as
displayed in Galaxy:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005640.html
and:
On Thu, Jul 7, 2011 at 7:14 AM, colin molter colin.mol...@gmail.com wrote:
Hi all,
i am trying to use a local instance of my galaxy to pre-format data stored
at sra-ncbi.
Does anyone has a working pipeline that (s)he could share.
Here is the pipeline I am using, with some questions.
1/
Hi all,
This new feature looks very exciting for tracking reproducibility -
now in theory both the tool wrapper version (explicit in the XML)
and any underlying tool version will both be recorded:
https://bitbucket.org/galaxy/galaxy-central/changeset/84b20f29dfdf
I have updated the NCBI BLAST+
On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa
samuel.la...@scilifelab.uu.se wrote:
One follow up question then:
The #if#else syntax, in for example this tool example:
...
... is that something that you galaxy parses itself (tried to grep for some
matching-code, but found nothing so far),
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