I'm trying to set up a mechanism to copy a local file using a setuid
executable, based on whether the registered user has read access to the local
file in question. Is there any means for a tool to know the registered user
who is running it?
David Hoover
Helix Systems Staff
http
When I try to load the megablast_wrapper tool, I get errors in the output:
AssertionError: Data table named 'blastdb' is required by tool but not
configured
I am totally confused how blastdb.loc should be configured. Is it one tab,
two, three?
David Hoover
Helix Systems Staff
http
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
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are sam_pileup.py
and sam_pileup.xml.
David Hoover
Helix Systems Staff
http://helix.nih.gov
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. This kills
two birds with one stone -- the download is smaller, and Safari doesn't mess
with the extension.
Now, does anyone know if it is possible to gzip a dataset from a history within
Galaxy prior to downloading?
David
On Sep 26, 2011, at 2:00 PM, David Hoover wrote:
Does anyone know how
arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; re
Any ideas?
David Hoover
Helix Systems Staff
SCB/CIT/NIH
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r.dev_off()
except Exception, exc:
stop_err( %s %str( exc ) )
David
On Oct 6, 2011, at 10:16 AM, David Hoover wrote:
Hi,
The scatterplot tool is broken in the distributed version. It works on the
main Galaxy server, but on our local installation it gives
Why do you need to create a proxy? The way I have ours set up is within a
virtual host:
VirtualHost
Location /
AuthName Helix Systems
AuthType Basic
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPUrl
I'd love to know answers to this question as well. So far, all I've done is
create two tools for copying files between Galaxy and a user's personal
directories using a rather dangerous setuid executable.
I have mulled over two possibilities for this problem. One is to run Galaxy as
root.
under 'Galaxy main tool
shed', I can get to any of the repositories listed at the Galaxy main toolshed.
Is this a bug or a feature?
David Hoover
Helix Systems Staff
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this in the .bashrc file for the Galaxy user then restart your server.
David Hoover
Helix Systems Staff, NIH
On Mar 27, 2012, at 4:31 PM, Xu, Jianpeng wrote:
Hi,
I have installed the local galaxy and tried to run draw quality score
boxplot.
It showed the error message:
Could not find
have practical unique role_id/user_id to
data associations?
Of course, I could just delete the old user and say too bad...
Thanks,
David Hoover
Helix Systems Staff, CIT/NIH
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of
localhost?
David Hoover
Helix Systems Staff
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.
Thanks!
Greg Von Kuster
On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to
use a job runner other than the local runner? The tool_id for the
toolshed tool isn't honored in universe_wsgi.ini the way the default
tools
to the default job runner.
Can this be changed so that the configured job runner remains the same after
reloading the toolshed tool?
On Jul 23, 2012, at 5:02 PM, David Hoover wrote:
OK, forget what I said earlier. I was watching for a different toolshed tool
than what I reconfigured. Never mind, using
I recently switched from galaxy-dist to galaxy-central as the source of my
local install (version 7427:cb9272041d95). When I delete a dataset from a
history, all the delete icons disappear from the datasets. They come back if I
refresh the page. Has anyone else noticed this?
David Hoover
with my local
install.
Is there some option or modification that I need to enable to allow access to
the generated HTML/PNG files in the database/files/000/database_###_files
directory?
David Hoover
Helix Systems Staff
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Is anyone working on adapting the GATK tools for a more recent version of GATK?
The distributed version is 1.4, and GATK is up to 2.1.
David Hoover
Helix Systems Staff
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hard-code the path in the xml tool file, but rather have a default location for
other executables and jar files. How should this best be done?
David Hoover
Helix Systems Staff
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I just recently updated to the latest version of galaxy-central, and when
I started galaxy, the tools were not listed on the left panel. I could
rerun old jobs from my history, however. Why are the tools not listed?
David Hoover
Helix Systems Staff
the drmaa jobs are run using the default Galaxy user.
Weird.
David Hoover
Helix Systems Staff
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This script is used multiple times, so you might want to make sure that this
change won't cause files to become readable that you would prefer remain
unreadable.
From the log output, it looks like files are chmod'd to the user, then later
back to the Galaxy user. Is there somewhere else
While I've got you on the line, do you know why enabling the real user method
blanks out the jobName for the PBS job? The jobName is set if the jobs are
submitted as the Galaxy user.
David
On Oct 3, 2012, at 11:03 AM, Nate Coraor wrote:
On Oct 3, 2012, at 10:06 AM, David Hoover wrote
message:
Not Found
The resource could not be found.
No route for /repository/browse_categories
Clicking on 'Repositories' gives this error:
This link may not be followed from within Galaxy.
Beyond this, can the toolshed use externally authenticated users?
David Hoover
Helix Systems Staff
How should I configure my local galaxy to allow access to sub-files in
/datasets/[hashcode]/display/? FastQC is still broken on the latest build.
This issue was reported by others as well.
David Hoover
Helix Systems Staff, CIT/NIH
Begin forwarded message:
From: David Hoover hoove
In the Add or Replace Groups tool for picard, if the read group platform unit
is left blank, the read group sample name is lost as well. Must all the read
group tags be set with this tool? Can some of them remain blank?
David Hoover
Helix Systems Staff, CIT/NIH
/spin1/users/galaxy/galaxy1/lib/galaxy/model/__init__.py, line
13, in module
import galaxy.datatypes.registry
File /spin1/users/galaxy/galaxy1/lib/galaxy/datatypes/registry.py,
line 9, in module
import gmap # added for gmap tools
ImportError: No module named gmap
What is missing?
David
, Dannon Baker wrote:
Is this a fresh clone from galaxy-dist or have you pulled it from
somewhere else? It looks like your galaxy clone's
lib/galaxy/datatypes/registry.py has been altered to have an extra
import, 'gmap', for gmap tools.
-Dannon
On Wed, Mar 6, 2013 at 12:08 PM, David Hoover hoove
I've installed the latest version of galaxy, and the admin column won't
scroll. I can't see any of the toolshed functions unless mybrowser is
expanded beyond the size of my desktop display. Is there something wrong?
David Hoover
Helix Systems Staff
it
be?
David Hoover
Helix Systems Staff
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To search
support for such a feature.
David Hoover
Helix Systems Staff
National Institutes of Health
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When a file is uploaded via FTP, and the file is compressed using gzip, the
file is uploaded and decompressed on the fly; however, the gzipped file is left
on the FTP server, rather than being deleted as normal. Is this a bug?
David Hoover
Helix Systems Staff
After the latest update, the Manage library permissions page is broken. The
Roles not associated boxes are pushed to the left of the frame, and the
double arrow buttons are misplaced down the page. This occurs under Safari
(5.1.10) and Chrome (31.0.1650.57) on a Mac running OS X 10.6.8.
of files created in the job_working_directory that start with
'metadata_', some of which contain the unicode.
Is there anything I can do to fix this?
David Hoover
Helix Systems Staff
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$TMPFILE 2
as a temporary workaround.
No idea if this is applicable in your case?!
Cheers,
Christian
*
changeset: 11219:5c789ab4144a
branch: stable
tag: tip
On 05.12.2013 17:29, David Hoover wrote:
I have installed the ngsplot galaxy tool from
http
=
cat -v $TMPFILE 2
as a temporary workaround.
No idea if this is applicable in your case?!
Cheers,
Christian
*
changeset: 11219:5c789ab4144a
branch: stable
tag: tip
On 05.12.2013 17:29, David Hoover wrote:
I have installed the ngsplot galaxy tool from
http
PM, David Hoover hoove...@helix.nih.gov wrote:
Right, nevermind, 'hg log' listed that changeset 10953:e786022dc67e.
Changing DEFAULT_ENCODING to 'latin-1' in lib/galaxy/util/__init__.py worked.
Do I need to alter ALL the MySQL tables to UTF-8, or just a selection of
tables? Will future
be happy to work around a
limitation in the mysql connector by adding a config option to Galaxy
if I were certain that there was a bug in the mysql connector.
-John
On Thu, Dec 5, 2013 at 12:55 PM, David Hoover hoove...@helix.nih.gov wrote:
John,
I stopped galaxy, then ran ALTER DATABASE
Are numpy and scipy included with the standard python modules/eggs
supplied by galaxy?
David Hoover
Helix Systems Staff
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forcing users to restart their jobs.
David Hoover
Helix Systems Staff
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' in the MySQL database.
Is there a better way of dealing with 'new' jobs?
BTW, our Galaxy instance was updated about two weeks ago.
Wondering,
David Hoover
Helix Systems Staff
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31, 2014, at 12:20 PM, Ido Tamir ta...@imp.ac.at wrote:
In my case it was uncompleted metadata in one of the input files.
(but maybe it was not new state but something else?)
HTH,
ido
On Mar 26, 2014, at 5:25 PM, David Hoover hoove...@helix.nih.gov wrote:
I have many jobs stuck
I saw the same phenomenon. I think it stems from the current version of
compute_q_values pointing to unavailable revisions of both R and the
bioc_qvalue R package. Whoever maintains the compute_q_values needs to
straighten out the revision ids.
David Hoover
Helix Systems Staff
National
Are there any tools available for transferring files using Globus? There’s
nothing in the toolsheds, but there was a lot of chatter a few years ago.
David Hoover
Helix Systems Staff
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What is the display_at_callback configuration setting, and how does it work?
Can it be used as a workaround for remotely authenticated instances of galaxy?
David Hoover
Helix Systems Staff
NIH
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that can be done to fix the problem, other than going into the database and
changing the tool_dependency.status from 'Never installed' to 'Installed' and
manually creating the subdirectories?
David Hoover, PhD
Helix Systems Staff
Hi,
I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I
realize I may be reinventing another wheel. Has anyone else created a tool for
STAR? There's nothing else in the toolsheds for it yet.
David
David Hoover, PhD
Helix Systems Staff
SCB/DCSS
datatypes?
It's always easier to build thing from comparison, rather than from scratch.
David
David Hoover, PhD
Helix Systems Staff
On Sep 24, 2014, at 4:14 PM, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi David,
yes there is inital code in the https://testtoolshed.g2
chimeric SAM
file?
David Hoover
On 9/24/2014 7:03 PM, Ross wrote:
Hi All,
That (fubar in testtoolshed) star wrapper was derived from one
originally written by Jeremy Goecks. I modified it for multiple inputs
and added a few tweaks and it has been in production use in our group
for about 6 months
.
David
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
On Sep 26, 2014, at 4:13 AM, Ross ross.laza...@gmail.com wrote:
Hi David.
I've not needed that workflow so haven't a solution for you and no, it
doesn't do anything
Why isn't there a datatype for a directory of files? This seems like such a
simple thing. If an executable generates or expects a directory as its input
or output, why must a fancy complicated composite datatype be created to handle
this?
David Hoover
David Hoover, PhD
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