substitute or replace a value?
by David Hoover
Is there a tool for doing a global or column-based substitution in a text or tabular file? For example, replace all instances of the number 2 in a column to a number 1?
David Hoover
Helix Systems Staff
http://helix.nih.gov
11 years, 9 months
MarkupSafe egg cannot be fetched
by Edward Kirton
hello, after pulling the latest changes from galaxy-central, i get the
following error:
WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched
$ python scripts/fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
11 years, 9 months
DB access and passowrd field
by Bossers, Alex
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 of course) when providing the details for access like address:port, username and password.
Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages.Or is this a bad thing to pursue anyway?
Thanks for any directions.
Alex
11 years, 9 months
Could anyone body tell me why our C program do not work in galaxy
by liyanhui607
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 shortest-path.xml is as follow:
Could anybody tell me what is wrong ? why it does not work?
Thank you very much!
Best Wishes!
Yan-Hui Li
<tool id="shortest_path_1" name="shortest_path">
<command interpreter="C">./shortest_path $infile1 $output </command>
<inputs>
<param format="text" name="infile1" type="data"
label="
expressed_genes_20101024.hprd8_biogrid-2.0.58.adj_matrix.txt
"/>
</inputs>
<outputs>
<data format="tabular" name="output" />
</outputs>
<tests>
<test>
<param name="input" value="1"/>
<param name="input" value="../GEO_dataset/expressed_genes_u133a.6k_u133p2.8k_20101024.txt"/>
<param name="input" value="../ppi/hprd8_biogrid-2.0.58.ppi.txt"/>
<output name="out_file1" file="expressed_genes_20101024.hprd8_biogrid-2.0.58.ppi.txt"/>
</test>
</tests>
</tool>
11 years, 9 months
NLStradamus wrapper (for nuclear localization signals)
by Peter Cock
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 Galaxy.
I would release this to the Galaxy Tool Shed now, but the tool's author
Alex Nguyen Ba tells me he hopes to have an update released fairly
soon which should include a native tabular output - probably with a
richer column structure. So rather than having to change the tool
output and potentially break workflows, I plan to wait till then.
However, if anyone wants the wrapper before then, drop me an email.
Regards,
Peter
References:
A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. NLStradamus:
a simple Hidden Markov Model for nuclear localization signal prediction.
BMC Bioinformatics. 2009 Jun 29;10(1):202.
http://www.moseslab.csb.utoronto.ca/NLStradamus
11 years, 9 months
Galaxy tools' priority level (nice)
by Peter Cock
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 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 place:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationSca...
Thanks,
Peter
11 years, 9 months
Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ... SVG!
by Peter Cock
On Thu, Apr 21, 2011 at 10:50 AM, Pieter Neerincx
<pieter.neerincx(a)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.neerincx(a)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 support is pretty good nowadays especially in FireFox
>>> and Opera. Safari, IE and Chrome have only partial support, but
>>> for simple charts without 3D filters it works fine. I've added SVG
>>> as a datatype to my Galaxy and this works great. You won't need
>>> a plugin; in fact the old Adobe SVG plugin is depreciated already
>>> for a few years now and no longer compatible with recent browser
>>> versions.
>>
>> I looked at SVG about a year ago, and was pretty impressed.
>> I did run into some issues, particularly with links, and opted to
>> use PNG files in the end. Since then we've finally dropped IE6,
>> so hopefully SVG would be safe now.
>>
>> Are your changes to add SVG as a datatype to Galaxy public?
>> I'd like to suggest that be merged to the trunk.
>
> I simply added this line to my datatypes_conf.xml:
>
> <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
>
> I didn't make a sniffer as I don't have a use case for users
> uploading SVGs, so I didn't have to create a Python class and
> SVG is just another instance of galaxy.datatypes.images:Image
> from a plain vanilla Galaxy.
That makes sense if the sniffer is only used on upload.
> To make sure the client displays the SVG you may have to add
> the SVG mimetype to your web server's config too. Where this
> is defined may differ per linux distro. I use apache as a proxy
> and had to add
>
> image/svg+xml svg svgz
>
> to /etc/mime.types.
Thanks for the details - it looks simple enough to add here too.
If/when any SVG producing tools are added to Galaxy or the
Galaxy Tool Shed, then it would be nice to have this done in
the main repository.
>>> The nice benefit of SVG in addition to not needing a plugin is
>>> that the image can scale with the surrounding text if you zoom
>>> in your browser (without loosing resolution).
>>>
>>> The disadvantage is that although my users know what a PDF
>>> file is and can process them for posters/manuscripts, most of
>>> them never heard of SVG and get stuck when it doesn't import
>>> into PowerPoint et al. :(
>>
>> Do they cope with PDF?
>
> Well, they know how to view and print one :). Importing them
> directly into PowerPoint and Word is just as problematic though,
> so that usually involves opening the PDF in a different program
> and copy/paste or exporting to another format. Still a hassle, but
> they manage...
Getting a PDF into PowerPoint or Word is easy on a Mac ;)
But yes, point taken - even though a PDF is easier to work with
than an SVG (or a postscript file), it can still be a hassle.
Peter
11 years, 9 months
Access control for galaxy
by Raghuraman Ramamurthy
Hello,
I would first like to thank and appreciate the Galaxy team for their
efforts.
I want to clone galaxy and host it in my website. In doing so, I want to
restrict the users who use galaxy on my website. So, is there any access
control module which could be integrated with galaxy, to make it secure and
grant access to only a set number of people.
Thanks,
Raghu
11 years, 9 months
Sample Tracking: How datasets are transferred from Sequencer to Galaxy
by Joe Cruz
Hello,
I was hoping someone could explain the process of how a dataset is
transfered from a configured Sequencer to a Galaxy library within sample
tracking. Particularly how RabbitMQ, API keys, transfer_manager_port and
enable_sequencer_communication (in universe_wsgi.ini file) work in this
process.
Your help is greatly appreciated!
Thanks
Joe A. Cruz
11 years, 9 months
