This is a using-the-API question; not sure if it belongs in galaxy-dev or
galaxy-user !
galaxy-dev is best because it's dealing with the development of Galaxy.
There seem to be two ways to retrieve metadata for a dataset, one in the
Histories API and one in the Datasets API. They return
Historical reasons only; this should be fixed.
And this is now fixed. Take a look at these changesets for details:
https://bitbucket.org/galaxy/galaxy-central/commits/579c0b64e463918691bb38e718af8d70dd6f9fa7
The tools API, incomplete as it is, could be used to automatically generate a
list of tools for a single instance.
J.
On Mar 4, 2013, at 5:37 AM, Hans-Rudolf Hotz wrote:
On 03/03/2013 05:18 PM, Dave Clements wrote:
Hi Bernardo,
I'm intrigued by this idea. It might be possible to
To perform bias correction using sequence data in
Cufflinks/Cuffcompare/Cuffdiff, you'll need to set up and add entries to
sam_fa_indices.loc
Of course, this isn't the most intuitive place, and we're planning to improve
loc file structure and usage in the future.
Best,
J.
On Mar 1, 2013, at
again
Best wishes, Peter
On 27/02/13 18:33, Jeremy Goecks wrote:
Thanks Peter. I've added your patch to the Trello card tracking
incorporation of community contributions to the Bowtie wrapper:
https://trello.com/c/TdYxdbkm
Best,
J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote
Attached to the card, thanks Peter.
J.
On Feb 28, 2013, at 11:14 AM, Peter Briggs wrote:
Hi Jeremy
No problem - zip file with the two patches is attached, please let me know if
there's a problem.
Best wishes
Peter
On 28/02/13 15:07, Jeremy Goecks wrote:
Hmm, I don't see a patch
Thanks Peter. I've added your patch to the Trello card tracking incorporation
of community contributions to the Bowtie wrapper:
https://trello.com/c/TdYxdbkm
Best,
J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie
what you described be accepted?
Any thoughts you or anyone has on the future direction of composite
datatypes in general would be appreciated?
Thanks for your time,
-John
On Fri, Oct 12, 2012 at 2:44 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Hi Jim,
This is nice
I see where I would use the *.ebwt files in the bowtie_index.loc file.
But I'm not sure what to reference in the bowtie_index_color.loc
file? (The same *.ebwt files??)
You need to download the colorspace indices separately:
http://bowtie-bio.sourceforge.net/index.shtml
Good luck,
There is some test data for hg19 on the RNA-seq exercise:
https://main.g2.bx.psu.edu/rna-seq
Best,
J.
On Feb 20, 2013, at 6:47 AM, Sachit Adhikari wrote:
Hi,
I need a test_data for Tophat with the hg19 reference genome? The test_data
from this website
But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file:
mm10mm10mm10
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index
You need:
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
J.
Why isn't it looking in that
After discussing this with Getiria, I think what is needed here is a way to
use FTP to upload compressed histories from the import screen as is available
from the upload data tool. The problem we're currently experiencing is that
when we try to upload a compressed history where the
,
I was successfully able to run the test data from the tophat2 website in
command line. I think there's something wrong with the reference genome. I
have correctly specified the path of reference genome? What's the problem I
am facing?
On Thu, Feb 14, 2013 at 1:44 PM, Jeremy Goecks
This is not a known bug. For questions related to Tophat errors, you might try
the Tophat mailing list:
tophat.cuffli...@gmail.com
Good luck,
J.
On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote:
Galaxy is working fine in command line whereas in Galaxy at last i got this
error:
the same problem and regarding settings I
haven't changed a thing of Tophat2. What might be causing this error?
Thanks
On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
If the other outputs are fine, then the problem is likely with your data
and/or your
This is a bug, and it's been fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/db08c095de0c249f3a6cde62f254c104de1fb6ea
Thanks for pointing it out,
J.
On Feb 13, 2013, at 8:25 PM, Anthonius deBoer wrote:
Hi,
One very cool feature was to be able to search
Shall I replace:
/orig/path/hg19hg19hg19
/depot/data2/galaxy/bowtie2/hg19/hg19
with
hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
Yes, that's correct.
Finally, please email only galaxy-dev with questions about local installations;
Also, do I have make all the reference files executable?
No, that's not necessary.
Best,
J.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists,
Error in tophat:
[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
---
[2013-02-13 02:02:43] Checking for Bowtie
Bowtie version:2.0.6.0
[2013-02-13 02:02:43] Checking for Samtools
Samtools version:
?
Thanks,
Sachit
On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Shall I replace:
/orig/path/hg19hg19hg19
/depot/data2/galaxy/bowtie2/hg19/hg19
with
hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence
I will try to reproduce. In the meantime, can you please check the JavaScript
console and forward along any errors that you see?
Thanks,
J.
On Feb 12, 2013, at 11:15 PM, Anthonius deBoer wrote:
Hi,
I had created a trackster vizualization that had not finished indexing yet,
So we did the following:
Downloaded the data
Added the paths to .loc file
restarted galaxy
We still are getting the following error:
2: Extract Genomic DNA on data 1
empty
format: fasta, database: hg19
56 warnings, 1st is: Chromosome by name 'chr22' was not found for build
'hg19'.
Hi Ricardo,
This tool requires external data that you'll need to configure. Here's how:
(1) download the 2bit file from UCSC for your genomes into a local directory
from here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
(2) add an entry like this to alignseq.loc (note that you'll
is the problem? I have
certainly mis-understanded your explaination.
Thanks.
julie
2013/2/6 Jeremy Goecks jeremy.goe...@emory.edu
Unfortunately using wget won't work in this case. The reason you have access
to the history is your Galaxy cookie, which isn't shared with wget/curl.
You'll
This is likely a permissions issue: importing your history into another Galaxy
instance requires the history to be accessible. Here's a solution that, while
ugly, should work:
(1) Make the history accessible by going to Share/Publish and clicking the
option to make it accessible.
(2) Export
work. I have the same error.
Sorry and thanks for the creation of the card.
Julie
2013/2/6 Jeremy Goecks jeremy.goe...@emory.edu
This is likely a permissions issue: importing your history into another
Galaxy instance requires the history to be accessible. Here's a solution
that, while ugly
with html code
thanks again.
Julie
2013/2/6 Jeremy Goecks jeremy.goe...@emory.edu
Ah, I see the issue: the Cistrome instance cannot be used anonymously
(without login). It's not possible for one Galaxy instance to work with
another instance's history because instances work with objects
Hi Luobin,
This isn't yet possible but is planned: https://trello.com/c/KxlQK0FB
Best,
J.
On Feb 6, 2013, at 2:47 PM, Luobin Yang wrote:
Hi, Galaxy developers,
I would like to have the parameters on the web interface to be packed into
sections for a tool. Is there a way to do this? There
My outputs section in the tool's xml file is:
outputs
data format=HTML name=fred_report label=generating FRED report.../
/outputs
You should set the output format to 'html' — all lower case. Galaxy has a list
of known dataset types in datatypes.conf, and your output format should
All works great, but I was hoping that there's an easy way to remove the
preview text box from the resulting History pane item (it currently shows
the unrendered html tags)?
This should not be happening. If your tool's output dataset has type HTML,
the peek (preview) should say 'HTML file'
On Jan 31, 2013, at 8:15 PM, Guest, Simon wrote:
Dear Galaxians,
We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is
the expected version, as I can't find any statement about what is required in
the Galaxy tool dependencies for RepeatMasker.
Anyway, when a job
So my quick hack broke this:
https://bitbucket.org/galaxy/galaxy-central/commits/0ec7f0b6dec8707b6f4d114468367c9131e61200
To fix this and related issues, I finally took the step of unifying all
builds and build information into a single Python data structure:
So my quick hack broke this:
https://bitbucket.org/galaxy/galaxy-central/commits/0ec7f0b6dec8707b6f4d114468367c9131e61200
To fix this and related issues, I finally took the step of unifying all builds
and build information into a single Python data structure:
please find attached a small patch that add the gen_image()
functionality to the export-workflow UI.
Thanks for the contribution. I committed a modified version of it:
https://bitbucket.org/galaxy/galaxy-central/commits/0e064a23864c846483b35f893cf0a769dedf24f1
Specifically, I (a) used
Adding the attribute
target=_top
to your URL will load the URL in the main browser window rather than a frame.
E.g.
a href=controller/action target=_topLoad result in top window/a
Best,
J.
On Jan 21, 2013, at 7:24 AM, Paul Boddie wrote:
Hello,
Is there a convenient recipe for
Two things confuse me about this. First, the tools I want to use are
not listed under the list of tools with dependencies.. but I still
need to install? what is the difference then between tools with
dependencies and all the others?
If I understand you correctly, here's the answer: tools with
I hope I have the correct place to ask for assistance.
Yes, this list is a great place to ask questions about local Galaxy instances.
I've been trying to use a local install of Galaxy. I can upload data and
convert formats (FASTq to FASTA) but can't use fasta manipulation tools like
width
read in gzipped FASTQ files in the STAR wrapper without
writing an external Python script or the like?
Thanks,
Patrick
Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Gesendet: Freitag, 18. Januar 2013 04:37
An: Sorn, Patrick
Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu
I have a very basic STAR wrapper that works:
https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default
For now, the wrapper does two things: maps RNA-seq reads and identifies
chimeric reads/junctions. There are tons of
I'd also been been worried about a similar requirement to ensure reviewers
could have anonymous access to software run as a service. In that case
even providing dummy accounts to the reviewers might not have been
allowed (since the administrator could easily 'spy' on what the reviewers
did or
Can you reproduce this behavior on our public server? If so, it'll be much
easier for us to take a look at the issue.
If you can't reproduce on our public server, then providing as many details as
possible about the problem will provide the best chance for the list to help
you. For instance:
Shared/published visualizations should be able to be used completely
anonymously, so that shouldn't be a problem. (Let us know if you find
otherwise.)
Workflows, however, are tied to user accounts, so using them requires a login
for now. Viewing workflows anonymously should be possible,
but the job listing in the
history is red, and the output is not available for input into other tools.
I’ve tried this on other tab-delimited files and it does the same thing.
Mark
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Monday, January 14, 2013 12:58 PM
with expression c3-c2+1
Kept 100.00% of 96 lines.
Thanks
Mark
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Monday, January 14, 2013 2:56 PM
To: Rose Mark USRE
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] text manipulation Compute tool error
If you click
Trying to fix Trackster on our Galaxy, I noticed that my browser (Firefox)
catches a lot of warnings, also on properties of CSS that I thought would be
especially for Firefox.
Can this cause lagging while using Galaxy? (some of our users experience slow
browsing on our Galaxy).
No, these
These bugs have been fixed in our development repository (galaxy-central) and
will be available in the next distribution, which should occur in the coming
week.
Thanks,
J.
On Jan 7, 2013, at 6:23 AM, MONJEAUD wrote:
Hello all,
I am using my own Galaxy instance and I had a problem with
This thread addresses your issue:
http://dev.list.galaxyproject.org/tophat-option-transcriptome-mismatches-not-recognized-td4657568.html
In the future, please use the mailing list search before posting your question.
You'll save time for both yourself and others.
file_name: /galaxy-central/database/files/000/dataset_733.dat
This is the dataset location on the filesystem (perhaps relative . If you
script is running on a machine that has access to the filesystem, you should be
able to simply copy it.
Best,
I don't understand why the option is offered in the galaxy UI if it's
not available, or is there some kind of bug, or wrong version of
tophat2?
The parameter has been deprecated in recent versions of Tophat; the wrapper has
been updated in -central changeset 4b4ea9952336 to reflect this.
J.
Hi
I am doing NGS analysis in our local galaxy, I would like to access the
output files for further analysis.
I do have an account on the server where galaxy is installed, so I would like
to access the output files without actually downloading them( aince they are
huge). Can you
I'm confused. So I installed tophat-2.0.6.Linux_x86_64 which seems to
contain tophat and tophat2.
tophat2 redirects to tophat, which is tophat version 2.X.X
Can't galaxy use that tophat?
You can, but you need to use the Tophat2 wrapper, not the Tophat for Illumina
wrapper. And, when you
Please see the Megablast section on this page for instructions about getting
and adding target databases to Galaxy:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Best,
J.
On Dec 10, 2012, at 2:59 PM, greg wrote:
I have a fresh install on our cluster.
I'm trying
Are there any included with Galaxy, or do I need to download a
database?
You need to download them.
Could you guys point me to a good file to test with?
Following the directions you sent I got to the point of downloading a
file. I tried download
Unfortunately, no solutions right now; currently, screenshots are best that can
be done. One trick we often use for publications/posters is zooming, taking
multiple screenshots, and then composing them together; ugly, but pretty
effective for showing details.
We have some ideas about how to
I was thinking whether I could establish the same from using the DB access
directly!? Or would that be too dangerous? In the past I have tried to
transfer the user tables from an old instance into a fresh onebut failed
due to all sorts of unpredictable errors..
We (the Galaxy team) do
(New feature discussion belong on the -dev list.)
This is not possible now but is pretty simple to do in the future:
(a) abstract the import/export history functionality into the UsesHistoryMixin;
and
(b) make import/export available via the API.
I've made a Trello card for this:
if dynamic options allowed a function to be used for
retrieving options from a dataset.
Best,
J.
On Nov 28, 2012, at 9:39 AM, S. Horsman wrote:
But how does that let me read from a binary file?
Bas
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: 22 November 2012 15:59
Thanks Jeremy, Are there any resources linked with Galaxy for viral genome
seq annotation ?
I'm not aware of any viral genome annotations resources integrated into Galaxy,
but NCBI (and others) have virus gene annotations that you upload into Galaxy
and use.
Best,
J.
Options and filters should work for what you need:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Coption.3E_tag_set
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.3E_tag_set
Best,
J.
On Nov 22, 2012, at 4:49 AM, S. Horsman wrote:
Hi All,
Because your questions are about a local installation of Galaxy, your email is
best suited to the galaxy-dev mailing list, so I've moved it there.
1. FastQC not running . gives an error and doesn’t run on groomed or
un-groomed FastQ file. The error message shows in the below pic.
I
Scatterplots will behave just as Trackster does: you'll be able to save
scatterplots and embed them in Pages.
Looking forward, the Galaxy team is in the process of developing a plug-in
framework for visualizations that will allow for arbitrary Web visualizations
to work with Galaxy. With this
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
I've seen this once or twice before but haven't been able to track down the
issue yet.
Here are two workaround that may help you out:
(1) Add the dataset to a
Two ideas:
(1) Use data libraries to import all UCSC data files, making sure to link data
rather than copy into Galaxy:
http://wiki.galaxyproject.org/Admin/Data%20Libraries/Uploading%20Library%20Files
(2) Set up a local table browser and modify the ucsc_tablebrowser.xml to point
to your local
Ah, sorry I missed this.
From IRC (weeks ago):
(03:15:01 PM) jmchilton: Ideally, what would the API uri for assigning
a tag to a histories dataset be? POST to
api/tags/tag_name/item_class(e.g.
HistoryDatasetAssociation)/encoded_id or POST to
While we're talking about the tags API, I'd also like to see if we can
think about the annotations API.
Can it be formulated in the same manner as the proposal for the tags api?
Yes, annotations and tags share the same structure, so it makes sense that the
tag API structure can be used for
What is the error that you're seeing on the server side?
I haven't tried this myself, but Brad Chapman suggested this example payload:
--
{tool_id: upload1,
history_id: identifier of history to use,
params: {file_type: vcf,
dbkey: hg19,
files_0|url_paste:
Kyle,
Tags haven't been implemented in the API yet. This is, of course, planned
development for the future.
J.
On Nov 9, 2012, at 7:56 PM, Kyle Ellrott wrote:
Are there any docs or examples about how to add/remove tags from items
via the galaxy web-api?
Thanks,
Kyle Ellrott
(BITS)
http://www.bits.vib.be
@bitsatvib
On 11/08/2012 04:14 PM, Jeremy Goecks wrote:
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that
you're seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that you're
seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote:
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Using my local instance, I was able to run Bowtie2 using a genome in the
history. This means the problem is likely with your local instance.
This appears to be the problem:
Error: could not open Nagenome.fasta
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build -f
JBrowse is fully client-side, so there is no jbrowse server we can use. Is
there a way to pass data to galaxy directly without the server? This
functionality could also be useful for desktop applications.
This isn't possible right now, though you could imagine using FTP with the API
to
Downloading data is handled in lib/galaxywebapps/galaxy/controllers/dataset.py,
method display(), which in turn calls this line:
--
return data.datatype.display_data(trans, data, preview, filename, to_ext,
chunk, **kwd)
--
Which, in most cases, calls display_data in
Where do I find info if the installed applications make use of multiple nodes
via MPI(etc) which would indicate the benefit of starting up X number of
nodes for faster processing?
You'll need to look at the individual tool documentation. In general, many
tools uses multiple cores, few use
Given that this doesn't seem to be happening on our public server or on local
instances, my best guess is that the issue is old code. Are you running the
most recent dist?
J.
On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote:
We are still getting empty TopHat output files on our Galaxy
last week.
Thanks!
Cheers,
Mo Heydarian
PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
414 Hunterian
Baltimore, MD 21205
On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Given
Whatever the file type I set for the gff file (gff3, gff or gtf), I get the
transcript_id error:
Traceback (most recent call last):
File
/home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py,
line 91, in
main()
File
Can you please share the datasets that are generating this errors?
Thanks,
J.
On Oct 24, 2012, at 4:19 AM, Joachim Jacob wrote:
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the
Passing it back to Jeremy, there is also a Javascript wrapper around the
tools API which might help:
https://bitbucket.org/galaxy/galaxy-central/src/tip/static/scripts/mvc/tools.js
Yes, the Galaxy team is working on a JavaScript binding to the API, and one of
the areas that we've done some
of the output of a liftover
file (which is in interval format).
https://dl.dropbox.com/u/18352887/Galaxy48-%5BSelect_first_on_data_23%5D.interval
As you can see, every interval is only one bp long...
Thanks
Joachim
On 10/24/2012 03:27 PM, Jeremy Goecks wrote:
Can you please share
Erik,
The API could be used for this.
Specifically, you could do an upload for the user from a URL via the tools API.
I know that Brad Chapman (cc'd) has done this successfully recently. Brad, can
you share the parameters used to do this?
Thanks,
J.
On Oct 22, 2012, at 3:21 PM, Erik
Yes, you should be able to use a single GFF for the complete genome.
This error stems from the same issue as before, namely that Galaxy is treating
your GFF file as GTF.
If you think your GFF is well formatted and there is an issue with Galaxy's
handling of GFF, please send me your GFF and
Try upgrading your Cufflinks binaries and see if that solves the problem; the
wrappers are designed to support versions 1.3+, but I'm not sure if they'll
work with older versions.
Best,
J.
On Oct 19, 2012, at 3:22 PM, Iry Witham wrote:
Hi Folks,
I have run into an issue with cuffmerge. I
Jonas,
Cuffmerge and Cuffcompare use the sam_fa_indices.loc for sequence data; this is
done for historical reasons.
You can see this if you take a look at the wrapper code:
galaxy_home/tools/ngs_rna/cuffmerge_wrapper.py
galaxy_home/tools/ngs_rna/cuffcompare_wrapper.py
Best,
J.
On Oct 19,
is not working? What might be the problem?
On Fri, Oct 19, 2012 at 9:01 AM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
You'll need to update the tool_data_table_conf.xml file in your Galaxy home
directory.
If you haven't made changes to the file, you can copy
Hi Jim,
This is nice and is a path forward for the immediate future.
That said, a couple extensions to Galaxy to better support composite datatypes
would enable cummerbund without the additional tools:
(i) extending the composite datatype to include definition of individual
outputs in the
Is there an easy way to add meta data to a dataset without having to resort
to coding it into the dataset definition?
I am looking for things beyond tags and just a simple key value pair
association would be enough...
Tags support key-value pairs using this syntax:
--
key:value
OR
My best guess is that these changes are occurring due to the changing corpus of
tool titles/descriptions/help text. (Search functionality hasn't been changed
in some time.)
I've tweaked the search parameters in -central changeset 18ab38e43d8b ,
specifically removing the minscore requirement,
Alex,
This is definitely an issue, but it is not currently high priority for the
Galaxy team.
We expect to move the Velvet wrappers to the tool shed in the near future, and
from there others can enhance the wrappers as needed. In the meantime,
community contributions to the Galaxy code base,
Looks great, committed in -central changeset 02fe49c3d251
Best,
J.
On Oct 6, 2012, at 6:31 PM, Björn Grüning wrote:
Hi all,
if we try to wrap a single script-tool, for example bismark [1], it has
its own version number and should be included in version_command.
I would like to ship
This looks fantastic Brad and we should be able to integrate it soon. I have a
couple questions, though, and I've noted them in the request's comments section.
Best,
J.
On Oct 4, 2012, at 3:44 PM, Brad Chapman wrote:
Hi all;
I've been thinking about ways to upload into user histories via
I explained the intent of that
code more in the comments and happy to answer any other questions.
Everything makes sense; I've accepted the pull request.
While you're looking at the API, would you also be willing to consider
this pull request:
That's a bug, fixed in cf93e8aa50f9
Thanks,
J.
On Oct 5, 2012, at 9:34 AM, Langhorst, Brad wrote:
On one particular history, I see this.
I am at 035583d94b11
I don't know why this happens on this history…
I cloned it, then re-ran one step.
I hope this stacktrace is helpful:
Alex,
We'll need more details if we're going to figure out what the issue is. For
example:
*are there certain dataset types that lead to a crash?
*what does the Galaxy log say (even if it's not interesting)?
*does the export job make it into the database and/or onto the cluster?
Any other info
We are using Sep 7 release of galaxy-dist. Strange enough we have a QA galaxy
which is almost identical to the production one except it uses /galaxy_qa as
prefix and a different database, but workflow editor works there.
The best idea is to update to the most current release (Sept. 20) and
What version of Galaxy are you using? I cannot reproduce the issue using the
most recent distribution or galaxy-central.
Also, there should be a full stacktrace in your paster.log. Can you share that
please?
Thanks,
J.
On Sep 27, 2012, at 11:05 AM, Liisa Koski wrote:
Hello,
I'm
Liisa,
My best guess is that this is fixed in the most recent distribution. Can you
please update your Galaxy instance to the Sept. 20 distribution and see if that
fixes the problem. If not, please let us know.
Thanks,
J.
On Sep 24, 2012, at 11:57 AM, Liisa Koski wrote:
Hello,
After
Try updating again and see if that fixes the issue. We've been refactoring
JavaScript dependencies, which may have caused some temporary problems.
In general, if you're going to use/track galaxy-central, you'll need to be both
persistent and patient because, as a development repository, things
The Cufflinks wrapper doesn't support v2.0 or greater yet. Please use v1.3.0
for now.
We expect to update the Cufflinks wrapper to support v2.0+ in the next couple
weeks.
Best,
J.
On Sep 25, 2012, at 5:34 PM, wormbuff wrote:
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie,
The bug manifests itself when running the tool with use Defaults selected
results in the following error:
cp: cannot stat
`/data/galaxy-dev/galaxy-dev/database/job_working_directory/000/281/tophat_out/fusions.out':
No such file or directory
It seems that somehow, the filter on the
Fixed in -central changeset 05a172868303
Thanks,
J.
On Sep 18, 2012, at 4:57 PM, Jim Johnson wrote:
The filter on the tophat2 fusions output wasn't being evaluated correctly
when settingsType is preSet since the param dict wouldn't then have an entry
for 'fusion_search'
$ hg diff
101 - 200 of 349 matches
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