? Also, any suggestions on how to organize the files in the
repository are welcome. Thanks.
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attachment
days (and counting). I have even
tried running the scripts with the -f option to force galaxy to
re-evaluate the datasets to no avail.
Any suggestions? Thanks.
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(and the number of datasets does not change in the saved
histories view).
Any thoughts on what might be going on here? Thanks.
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The patches have been put into a pull request.
Lance
Nate Coraor wrote:
Lance Parsons wrote:
For what it's worth, I ran into an issue with the use of /tmp as
well. When merging a lot of BAM files, /tmp filled up and the merge
failed. To make matters worse, since STDERR is redirected
:
Lance Parsons wrote:
I'm running a local instance of Galaxy that has been working quite
well. However, I've recently run into a problem when importing
datasets from a data library into a history. The Size on Disk of
the history grows by the size of the imported dataset, however, the
new dataset
the
copied HistoryDatasetAssociation is created, and whether the source
LibraryDatasetDatasetAssociation is itself deleted (which should be the
only way the resulting hda could be deleted).
Lance
Lance Parsons wrote:
Good catch, that does indeed seem to be the issue. And it only seems
to happen
:
select * from library_dataset where deleted=f and purged=t;
With those, I would think setting purged to f and then setting deleted =
f for the associated library_dataset_dataset_association records.
Lance
Nate Coraor wrote:
Lance Parsons wrote:
Good catch, that does indeed seem
/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy).
However, I can't figure out why BAM files work and VCF files don't. Any
advice or insight would be appreciated.
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do something like:
requirements
requirement type=packagebedtools/requirement
requirement type=binarygenomeCoverageBed/requirement
/requirements
Secondly, once this is sorted out, it would be nice to update the Tool
Config Syntax documentation. Thanks in advance for any advice.
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Lance
, and the Python library
pysam.
Lance, your tool doesn't seem to include any author information
like your name or email address. I'm inferring it is yours from the
Galaxy tool shed user id, lparsons.
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file to
match and add the new split option.
We could list this as three contributing authors if you both like?
Peter
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/lance_parsons/freebayes/) and given Daniel and
Greg access to it in hopes that would make things easier.Let me know if
there is a better way to coordinate, etc.
Thanks again.
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to
0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor
differences from your pull request. Please let us know if you
experience any issues installing or using the updated version (0.0.3).
Thanks,
Dan
On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote:
I have been using
).
Thanks for using Galaxy,
Dan
On Aug 31, 2012, at 11:47 AM, Lance Parsons wrote:
Thanks for the quick turnaround Dan. Much appreciated. When I tried
to test updating Freebayes from the toolshed, I get a message that no
updates are available. Perhaps it takes some time before
)
gets executed during installation.
2) Another issue is the inability to install Numpy as a dependancy to
HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH
when HTSeq is installed (or executed).
Any thoughts on how to address these issues would be appreciated.
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Lance
for the inconvenience on this.
Greg Von Kuster
On Aug 31, 2012, at 3:59 PM, Lance Parsons wrote:
Thanks for the explanation. That makes sense. I went ahead and
installed the new version along with dependencies in my development
environments and all went well. Then in production, the installation
automatically. It would
be great if you could update the Tool Shed repo. Thanks.
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diff --git a/tool_dependencies.xml b/tool_dependencies.xml
be of help.
Lance
Greg Von Kuster wrote:
Hello Lance,
See my inline comments.
On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote:
I've put together a tool wrapper for the htseq-count script that is part of the
HTSeq python package and uploaded that to the tool shed. However, I have
discovered
-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py',
line 103 in __init__
_(unknown revision '%s') % changeid)
RepoLookupError: unknown revision '4'
Lance Parsons wrote:
Thanks Greg. I used you're updated version and added numpy as a
separate dependency. It seems to work in my development
sure how you could be trying to update to 4. Did you
install 4 and are trying to get updates?
I've tried several things but am not able to reproduce this behavior,
so it's difficult to determine what may be causing the problem
Greg Von Kuster
On Sep 12, 2012, at 3:08 PM, Lance Parsons wrote
things a bit more robust, I suggest
adding bowtie2 as a requirement to the tophat2 wrapper. It also might
be a good idea to add versions to those requirements. I've attached a
small patch to do that (though it's fairly trivial).
Thanks.
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...
On Sep 13, 2012, at 4:41 PM, Lance Parsons wrote:
Actually, I think that is exactly the issue. I DO have
3:f7a5b54a8d4f installed. I've run into a related issue before, but
didn't fully understand it.
I believe what happened was:
1) I pushed revision 3:f7a5b54a8d4f to the tool shed which
from Mercurial (even version 2.3.3) do not seem to trigger
metadata refreshes in the tool shed, however, uploads of tar.gz files do.
Hope this helps.
Lance
Lance Parsons wrote:
I've run into this issue again, and I'm having a hard time working
around it. However, I have confirmed that at least
; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
Hope this helps.
Lance
Lance Parsons wrote:
I've run into this issue again, and I'm having a hard time working
around it. However, I have confirmed that at least some updates to
a tool in the tool shed will invalidate previously
AM, Lance Parsons wrote:
I'm sorry I wasn't more clear. I do believe that those links explain
the behavior I am seeing. However, let me try to describe it a
different way. It seems that there will, at most, be one installable
revision of a given version of a tool. Here I use revision to denote
/
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have installed (10) is not
longer considered a valid revision by the toolshed (I presume since it
is an older revision of with the same tool version).
Any help would be appreciated. Thanks.
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describe
above, we'll need more details as to the process you used in order to determine
the cause of the problem.
Greg Von Kuster
On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:
I recently updated the htseq-count tool in the Galaxy toolshed to version 0.3.
This version has some functional
running mercurial version 2.2.3 and
Python 2.5. What's your environment?
Greg Von Kuster
On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote:
Since I've had issues with workflow and the toolshed in the past, I
have changed my workflow so that my only interaction with the
toolshed is either
outside of the if
block, does indeed fix that issue
2) Fixing that leads the __check_user_jobs method to fail since it does
not check `self.track_jobs_in_database`, but instead assumes that jobs
are in the database, resulting in a different exception regarding
invalid columns.
Lance Parsons wrote
of it committed
(including this fix) some time this week. Thanks for figuring out
exactly what's going on here.
--nate
On Jan 18, 2013, at 5:28 PM, Lance Parsons wrote:
Just an update on this issue. Upon further investigation, it looks
like the dynamic job runner code in commit 6f3b4e8 broke this. I
will make it again a little closer to a perfect world :-)
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 12/17/2012 05:28 PM, Lance Parsons wrote:
Thanks for looking
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 12/17/2012 05:28 PM, Lance Parsons wrote:
Thanks for looking into this Greg. The environment where I'm having
this problem is our testing
, logging, etc. Any tips on generally acceptable
(supported) procedures for marking a dataset as deleted?
Of course, I'll make any of the enhancements available (and would be
happy to submit pull requests if there is interest).
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Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/11/2013 06:34 PM, Lance Parsons wrote:
I have posted an updated version of the htseq-count tool in the
toolshed that uses and updated version of the HTSEQ count package
(0.5.4p1
.. Thanks.
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file )
.. image:: ./static/images/count_modes.png
:width: 500
I believe that's all that is necessary.
Greg Von Kuster
On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote:
For one of my tool wrappers (htseq-count) in the toolshed, I point to
an image file in the Help section
Nate Coraor wrote:
On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote:
I have been running a Galaxy server for our sequencing researchers for a while
now and it's become increasingly successful. The biggest resource challenge for
us has been, and continues to be disk space. As such, I'd like
that are compatible. Thanks.
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by the update_time. I think files should be deleted by
the access time. Is it enough to resolve this problem by checking the
update_time of the HistoryDatasetAssociation table?
Thanks for your help,
X. Meng
Joint Genome Institute, LBNL
quote author='Lance Parsons'
Nate Coraor wrote:
On Mar 22
/
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Template Variables:
cutoff - the cutoff in days
email - the users email address
datasets - a list of tuples containing 'dataset' and 'history' names
Lance Parsons wrote:
Nate Coraor wrote:
On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote:
I have been running a Galaxy server for our
/mailinglists/
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RETURNING disk_usage;
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No problem, glad it was helpful.
Dannon Baker wrote:
Thanks for the bug fix, (and for the reminder that it was still
sitting in the inbox, sorry about that). I've verified the fix as
well and pulled it into -central.
-Dannon
On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons lpars
error:
http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picardowner=devteamchangeset_revision=e0232cbac965
Looks like this changeset is relevant:
https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
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it once I get a
chance tomorrow.
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Original message
From: Greg Von Kuster g...@bx.psu.edu
Date: 06/11/2013 10:00 PM (GMT-05:00
an issue on Trello
(https://trello.com/c/XYkqW3Lr).
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submitted an issue on Trello
(https://trello.com/c/XYkqW3Lr).
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for each migrated tool?
Thanks for any help or suggestions.
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these. Is there a bitbucket repo somewhere
to submit pull requests?
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these. Is there a bitbucket repo somewhere
to submit pull requests? Also, I'm not sure if this is best sent to
this list or put into Trello, etc.
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practice for adding a new genome? Updating
builds.txt or manual_builds.txt?
2) Can the manual_builds.txt file be generated from a sample and moved
out of source control? (I'll add a Trello card if this seems reasonable).
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was not ready for use as a job
input? I'd very much like to fix these datasets since having to
re-upload data libraries would be very tedious.
Thanks in advance.
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[mailto:galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Aaron Petkau
*Sent:* Wednesday, October 01, 2014 5:32 PM
*To:* Lance Parsons
*Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Jobs stuck in new state - Data Library
datasets to blame?
Are you attempting to upload datasets to a Data
https
to the httpd.conf and that appears to be working. Is there something
else I need to do? Should I patch the data_source tools to use https in
the xml tool definitions? Thanks for any advice.
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. Thanks in advance.
Lance
Lance Parsons wrote:
Thanks, that was the first thing I checked. However, restarting the
handler didn't help. Downloading the offending data and re-uploading
as a new data set and then rerunning using the new dataset as input
did work. Also, all other jobs continued
, I need to do to prepare for this update? Thanks.
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Thanks in advance.
Lance
Lance Parsons wrote:
Thanks, that was the first thing I checked. However, restarting the handler
didn't help. Downloading the offending data and re-uploading as a new data
set and then rerunning using the new dataset as input did work. Also, all
other jobs
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