Hi, Bruno.
As Björn points out, cross-toolshed dependencies aren't currently supported
but exporting (eg) package_r_3_1_1 as a capsule (make sure to include ALL
dependencies) from one toolshed and importing that capsule into your own
local toolshed brings all the sub-dependent packages so they
Rdata is binary and serialises R objects so I sure hope you don't have to
peek inside - probably needs most of an R environment - like rpy or
something.
A binary header signature magic number would be ideal - I checked a few
saved rdata files lying around here and all seemed to start with the
You might need to specify multiple command lines in a single shell action -
separated by ; like:
cd foo; perl foo bah; more something; cleanup
Otherwise you might just find yourself back in the temp installation
directory after each separate action
Ross Lazarus
Head, Computational Biology, Baker
?
On Thu, Sep 25, 2014 at 10:41 PM, David Hoover hoove...@helix.nih.gov
wrote:
Ross,
About the index files: It is way easier to have pre-built index files.
However, when running a 2-pass STAR run, a user will need to generate their
own reference index files based on the output SJ.tab.out file
is
a pain - best to write a data manager.
Ross Lazarus
Head, Computational Biology, Baker IDI, Melbourne, Australia
Pubs: http://scholar.google.com/citations?hl=enuser=UCUuEM4J
On Thu, Sep 25, 2014 at 6:39 AM, David Hoover hoove...@helix.nih.gov
wrote:
Why didn't I see these before? Hmm, I
Hi Christophe - there's a trello card for this at
https://trello.com/c/ClgcV0Sn - upvote and add your experiences please?
On Wed, Sep 17, 2014 at 8:01 AM, Christophe Antoniewski
christophe.antoniew...@snv.jussieu.fr wrote:
I am trying to move the package_r_3_0_3 repository owned by devteam
Hi, Kevin.
Yes. that looks like an interesting error message which might have been
caused because Galaxy currently requires a version of Python such as 2.7.8
(2.6+ will work fine) but it will not run under the newest Python v3
releases (eg Python 3.4.1)
(You may also have encountered a bug in that
and still no cluster options in megablast item. How can I see cluster
options in the page, for example, the page will let me choose to use local
server or a cluster.
Users can't control destinations for tool execution through any interface
at present AFAIK - tool destinations are automated
Your question was answered in the negative on biostar a few days back:
https://biostar.usegalaxy.org/p/8101/
Contributions welcomed.
On Sat, Jun 21, 2014 at 8:25 AM, Jones, Tyler William
tyler.jo...@coyotes.usd.edu wrote:
Hi,
I am working for USD Bioinformatics and trying to integrate
This syntax
*write.table(data1, file={$out_data}, *
might not do what you expect. The $ has to be outside the braces, but
they're not needed there anyway - something like this might work better:
*write.table(data1, file=$out_data,..*
When things don't work, it's always useful to check the
into your local Galaxy) for ordinary users to use in their
workflows.
Thanks,
Karthik
On Sun, Jun 8, 2014 at 6:25 PM, Ross ross.laza...@gmail.com wrote:
Hi, Karthik and John.
Some details on the tool factory for anyone interested.
Executive summary: it may be helpful in this context but only
for reporting this - if it persists on recent Galaxy code we'll need
to do some deeper investigation.
On Fri, Jun 6, 2014 at 11:32 PM, Malcolm Tobias mtob...@wustl.edu wrote:
Ross,
Thanks for the reply! Unfortunately I am the local Galaxy admin ;-)
I had tried installing the clustalw tool from
Hi Melissa,
The question in the title is easy to answer - most large galaxy instances
run (most) jobs on a connected cluster which is effectively 'background' I
guess so yes - all of them on cluster backed Galaxy instances might be a
reasonable response.
The questions in the text are more
Malcolm,
It looks like you have downloaded the wrapper and put it in your local
tools folder. We strongly recommend that you remove the tool_conf.xml entry
and get the local galaxy administrator to install the devteam clustalw
repository from the main toolshed. That should solve your problem -
Hi, Mark,
Perhaps you need to adjusted universe_wsgi.ini where it says:
# Add an option to the admin library upload tool allowing admins to paste
# filesystem paths to files and directories in a box, and these paths will
be
# added to a library. Set to True to enable. Please note the security
#
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with
your setup?
What errors do you see?
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
On Thu, Apr 17, 2014 at 10:43 PM, Saket
Hi, Jun and Sebastian,
This is not trivial, but it is already being done with some tools using the
method described at
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Single_history_output_Html_file_with_links_to_any_number_of_output_files_and_images
if
that can solve your
if a tool failed we all really benefit from seeing as much as we can - as
securely as we can.
Can we safely expose them somewhere protected?
On Thu, Feb 20, 2014 at 8:59 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Ketan - great news - all the best with your project...
On Tue, Feb 18, 2014 at 3:58 PM, Ketan Maheshwari ke...@mcs.anl.gov wrote:
Ross,
That's correct. It seems I tested on a cached copy of tool. Works now!
Thanks,
Ketan
On Mon, Feb 17, 2014 at 10:55 PM, Ross ross.laza...@gmail.com
Hi, Todd,
The search bar at https://wiki.galaxyproject.org/ is always a good place to
find stuff like
https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes?highlight=%28converters%29
I hope this gets you started
On Sat, Feb 8, 2014 at 12:22 PM, Todd Oakley
in your tool menu - until those
manually installed ones (which may depend on clustalw2 being on the path)
are removed?
On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga khm...@soe.ucsc.edu wrote:
Hi Ross,
Thanks for your email. I have clustalw2 working now - I installed the
clustal repository
file needed for the
tool to find it.
On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga khm...@soe.ucsc.edu wrote:
Hi Ross,
I did not detect any type of auto-install (?) After installing from
toolshed I did not find the binary under the /mnt/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos
path. I believe the documentation explains this
- if it's not clear please suggest some revisions ?
On Mon, Dec 2, 2013 at 9:18 AM, Karen Miga khm...@soe.ucsc.edu wrote:
Hi Ross,
That is listed as tool_dependency_dir = /mnt/galaxy/tools in my
universe_wsgi.ini file, and that did not contain
On Sun, Dec 1, 2013 at 2:23 PM, Ross ross.laza...@gmail.com wrote:
Just to confirm, you used automated installation via the admin menu -
search and browse toolsheds - test toolshed - etc ?
If you installed manually by downloading and unpacking the archive under
your tools/ directory, then yes
Hi, Karen - how did you install clustalw?
If not already done, can you please try installing the clustal
repository owned by fubar from the test toolshed through your Galaxy admin
interface - search/browse toolsheds? Please let me know how you go and if
there's a problem I'll try to fix it for
Hi, Jun.
The inbuilt parameter sanitizer can be controlled - see
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
The valid sub-tag allows precise control and you can specify eg
string.printable if you want ANY printable character in your parameter
Here's an
3.49874201497232e-08 1.09398957489501e-06 9.03556928822473 140 a href='
http://www.genecards.org/index.php?path=/Search/keyword/Mir153'Mir153/a
Categories
Statistics
On Sep 26, 2013, at 6:47 AM, Ross ross.laza...@gmail.com wrote:
+1
I think it's been a problem with some of my repos
Vipin,
Search works pretty well on the toolshed - I'd recommend a search for (eg)
'star' before writing yet another rnastar toolshed wrapper and dependency
package? There's an installable fubar package_rnastar and an rnastar
wrapper based on Jeremy's code mentioned below - but working AFAIK - at
Hi Tevfik,
Adam is right, but even easier assuming it goes smoothly, you should be
able to install an updated version 3.3 of JJ's previous 3.2 wrapper via the
Galaxy admin interface - test toolshed; SNP Analysis;
/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log
On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan
sridhar2bioi...@gmail.com wrote:
Hi Ross,
i Installed through admin interface .
for pysam and freetype it showed new... and rest installed
through the tool page in your admin interface.
The htseq dependency will contain the installation log I need to see.
On Wed, Aug 21, 2013 at 5:06 PM, Sridhar Srinivasan
sridhar2bioi...@gmail.com wrote:
Hi Ross,
I tried installing again it shows no item..
Also i couldn't find any .log file
/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
Hi, Richard,
I see you are looking in the main toolshed. I cant speak for fcarmia's one
but it doesn't do any dependency installation. The 'digital_dge' one was
deprecated - I've now deleted it.
The differential count models package in the statistics section of the test
toolshed -
Neil,
good news: the initial center panel renders static/welcome.html so easy to
change.
bad news: AFAIK no way to show a (dynamic) default tool form instead -
others may know more..
On Mon, Jul 29, 2013 at 5:03 PM, neil.burd...@csiro.au wrote:
Hi,
When Galaxy is started the centre
...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Wednesday, July 17, 2013 at 10:26 PM, Ross wrote:
AFAIK it's not yet possible, but a tool shed API to expose subversion
hooks for repository
Hi Nilesh,
A test_data folder and contents seem to be missing from your (eg) dev
repository - the docs at http://wiki.galaxyproject.org/Tool%20Shed include
http://wiki.galaxyproject.org/TestingInstalledTools which starts with:
Tool shed repositories that contain tools with defined functional
:
Hi Michael,
I think you will enter new ground with your tool. The closest tool that
will do something similar is Ross toolfactory, I think:
http://toolshed.g2.bx.psu.edu/view/fubar/toolfactory
For me one question is, do you really want to offer that service to
every user and is it save
lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl
, 2013 at 11:25 AM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
Ross,
Thanks for the comments.
I've already made my main tool tool_shed compatible. What I'm wondering
about is what do I do with the tools that my tool creates?
Sincerely,
Michael E. Cotterell
Ph.D. Student
(mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Wednesday, July 17, 2013 at 10:05 PM, Ross wrote:
Sorry if my post was rambling and unclear.
Here's the executive summary for what it's worth:
IMHO, a Galaxy tool that generates tools should emit them as tool shed
compatible artefacts
/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Unicode isn't handled nicely yet AFAIK so
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in
position 23: ordinal not in range(128)
might mean a http://www.fileformat.info/info/unicode/char/2013/index.htm -
overtyping these in an ascii text editor will remove them but this is a
/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
about that Ross. I would try your wrapper of edgeR and would
happily report you the bug. Can you make me the link of Galaxy Test
Toolshed?
Thanks,
Sachit
On Mon, Jul 8, 2013 at 11:51 AM, Ross ross.laza...@gmail.com wrote:
(Sachit, please don't cross-post to the dev and user lists
Hi Dan,
That's old code. Updating will probably help.
Logging level just takes disk space, but just in case you haven't followed
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance
leaving
debug = True uncommented used to fill
Did you try what was suggested below in my reply 5 days ago?
Ross ross.laza...@gmail.com
Jun 29 (5 days ago)
to *azuzolo*, galaxy-dev
Hi, Amanda,
If your previous version was very old, it may have lacked a parameter added
to universe_wsgi.ini some time ago to control universal sanitization of
HTML
Hi, Amanda,
If your previous version was very old, it may have lacked a parameter added
to universe_wsgi.ini some time ago to control universal sanitization of
HTML as a security precaution on public sites. If it's not already there,
could you try adding
sanitize_all_html = False
to your
at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
___
Please keep all replies on the list by using
Shashi,
Hans made a brave guess based on your vague question, but you'll probably
get better answers if you do us all a favour and make an effort to provide
unambiguous detail about exactly what you want to achieve.
If there is a working Galaxy tool that does what you need but using a
different
you hack
the tool into Galaxy itself or something. There is no documentation for
that.
On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar me_shash...@yahoo.co.inwrote:
Hi Ross,
thanks for the reply . actually i want to use TreeView as visulaization
tool.
TreeView X is an open source and multi
Shashi,
Beats me. Cloning the visualisation code would be a good start I'd
guess. It will not be trivial.
Others may have better ideas.
On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar me_shash...@yahoo.co.inwrote:
Hi Ross,
Actually i have to add the visualization which will be interactive
Hi Jens, the toolfactory (install from the admin menu - it's in the main
toolshed) allows admin users to paste and run arbitrary R scripts.
Yes, there are serious security issues exposing unrestricted scripting! So
the toolfactory only works for admin users and should never be installed on
?
AFAIK they need to be from the same subjects - so probably need some
thought to make it optimal for a biologist user
On Tue, Jun 4, 2013 at 8:39 PM, Saket Choudhary sake...@gmail.com wrote:
Thanks Ross and Peter. That worked.
I think I will keep the Python wrapper though, gives me more
, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser
Hi Saket
If you want to redirect the executable's stdout to a new Galaxy dataset
you've defined as $output, something like:
gt; '$output'
is a workable idiom for a command line AFAIK - you need to escape the
redirection '' character or you'll confuse the xml parser.
It's often possible to hack a
Hi, Saket.
Welcome aboard - help is always available here or irc if you're in the
right timezone.
https://chgr.mc.vanderbilt.edu/plato/https://chgr.mc.vanderbilt.edu/plato/steps/3
is
a brand new eQTL option from Marylyn Ritchie's group I stumbled across at
at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
-- Forwarded message --
From: מירב . mer...@gmail.com
Date: Wed, May 29, 2013 at 8:40 PM
Subject: Re: [galaxy-dev] installing galaxy
To: Ross ross.laza...@gmail.com
It worked!! Thank you very mach [?]
Merav
2013/5/29 Ross ross.laza...@gmail.com
Hi, Merav.
A fully functional
Buildbot can be triggered here
http://buildbot.g2.bx.psu.edu/builders/central-py2.7-linux-x86_64-postgres
manually
I think.
On Fri, May 10, 2013 at 10:56 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Is there a more optimal time to initiate this testing process to better
accommodate those in
Neil,
AFAIK, python will not load a module unless the relevant script file is
marked as executable by the current user?
Try something like:
chmod ugo+x scripts/db_shell.py
and see if that fixes your problem?
On Tue, Apr 30, 2013 at 11:50 AM, neil.burd...@csiro.au wrote:
Hi,
I'm trying to
Funny, it works for me.
One last thought: You do still have the distributed __init__.py readable by
your userid in /scripts so the module loader knows it's a python package
directory?
On Tue, Apr 30, 2013 at 12:05 PM, neil.burd...@csiro.au wrote:
Thanks for the info Ross
** **
But I
Hi, David.
does enclosing your XML in a CDATA section help? It should just get written
out without being interpreted, and it works for me in the toolfactory - the
contents still get written out but without the CDATA section.
configfiles
configfile name=loadTestxml
