Hi Alex,
Have a look at the 'sanititzer tag set' on the
http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax page. Caution
is urged when modifying these options. Please let us know if you encounter
difficulty.
Thanks for using Galaxy,
Dan
On Feb 16, 2011, at 5:22 AM, Bossers,
Hi Glen,
Sorry for the delay in response.
And how do I limit selections in an input drop down to just my specific file
type? I'm guessing I need to extend the Tabular class, but I don't need to
add any additional functionality at this point, I just want to limit how the
tools can be
Hi Assaf,
Just a quick note that the standard bowtie tool in Galaxy was enhanced in
changeset 5157:7a9476924daf to work on 'fastqillumina' and 'fastqsolexa'
variants in addition to the already possible 'fastqsanger'. In general, it is
not a good idea to have a tool accept dataset.ext=='fastq'
.) and reuse the underlying original
dataset file as the output (without writing over the file). This would be
significantly faster and not waste disk space, but it would require
enhancements to the framework.
Thanks,
Dan
On Mar 29, 2011, at 11:46 AM, Assaf Gordon wrote:
Hi Dan,
Daniel
Hi Martin,
You uncovered a bug with using check_values=false and tool output labels. A
fix was committed in 5289:b453988dce62; thanks for reporting the error.
However, there are a couple of issues with your datasource tool configuration
-- the most important being the setting of the tool_type
Hi Peter,
Yes, setting min and max values in the repeat tag should work as you need. As
you point out, it is probably not well documented, so please let us know if it
isn't working as you imagine it should.
Thanks for using Galaxy,
Dan
On Apr 19, 2011, at 6:47 AM, Peter Cock wrote:
Hi
I'll just chime in quickly with an agreement that FASTQ files should not have
dbkeys set. They don't yet belong to a build/reference genome version. Some
tools/workflows may currently require a FASTQ file to have the dbkey set, but
this should be considered a work-around for a defect in a tool
Patch Imported in 5618:b9fdb88da530.
Thanks!
Dan
On Mar 16, 2011, at 11:50 AM, Jim Johnson wrote:
Request is issue#494
https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch
I'm finding that some qiime metagenomics applications build HTML
:Daniel Blankenberg d...@bx.psu.edu
date:Thu Jun 09 11:26:41 2011 -0400
summary: Some fixes for interplay between DataToolParameter,
implicit datatype conversion and dynamic select
lists. Closes #491.
I guess there are downsides to running my development environment off
galaxy
say that finalized tools and e.g. tools submitted
to the tool shed should be vetted against galaxy-dist.
Thanks for using Galaxy,
Dan
On Jun 16, 2011, at 9:26 AM, Peter Cock wrote:
On Thu, Jun 16, 2011 at 2:23 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
If you were curious
Hi Hans,
Very sorry for the delay in response. The sample file that was included was
incorrect, but has been updated in changeset 5775:4220f8a5c571 and should now
display an interface.
If you would like to use or run the tool, you may find
Hi Brian,
This error is most likely caused by missing HDF libraries and the python Tables
module. You should be able to get the exact error of the conversion by looking
at the failed conversion history item (its hidden by default; under history
options, click 'show hidden datasets'). Please
Hi Amir,
If you are interested in adding a new datasource, take a look at:
http://database.oxfordjournals.org/content/2011/bar011.full
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
If you just want to add a file from an http/ftp location, take a look at the
Upload tool, under the Get
Hi Peter,
Sorry for the delay in response.
The outputs data actions tagset will allow you to set metadata, including
e.g. column assignments (start,end,strand,etc) for tabular (interval) files. A
somewhat complicated example of this is the cut tool
(tools/filters/cutWrapper.xml), which sets
Hi Shashi,
Have a look at:
http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial
And at the XML files in the directory: $GALAXY_ROOT/display_applications/
Thanks for using Galaxy,
Dan
On Aug 23, 2011, at 7:30 AM, shashi shekhar wrote:
Hi All,
I want to
,
Dan
On Aug 23, 2011, at 8:47 AM, shashi shekhar wrote:
Hi,
In Galaxy there is visualization option .how it works .Are documents are
available for visualization tool.
Thanks for Reply
Regards
shashi
On Tue, Aug 23, 2011 at 5:55 PM, Daniel Blankenberg d...@bx.psu.edu
Hi Ilya,
Tools should not ordinarily write to this directory, but will often read from
it. These files are generated by Galaxy's Metadata functionality. If you are
setting metadata externally (settings in universe_wsgi.ini) and using a
cluster, then this will occur as part of the tool/job
Hi Scott,
For information on adding Datasource tools to Galaxy, please see:
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
http://www.ncbi.nlm.nih.gov/pubmed/21531983
If your resource is using software that is already Galaxy-aware, you can often
take an existing xml configuration
Hi Ilya,
The JVM can be quite a pain when determining the best way to determine max
memory, however the underlying gatk_wrapper.py script was updated last week in
5970:20215fcf6da7 to allow using -Xmx or XX:DefaultMaxRAMFraction. Each of the
GATK tools are currently already set to use
:
The newest version of the Unified Genotyper has a –glm option which needs to
be set to both to call indels.
BTW, any interest in writing a wrapper for the Depth of Coverage tool?
Thanks,
Ilya
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Wednesday, September 07
Is this instance using the run job as user patch, and if so, does the user
running the job have permission to access the egg?
Thanks for using Galaxy,
Dan
On Sep 30, 2011, at 11:36 AM, Chorny, Ilya wrote:
The egg is there, but the error still shows up.
-Original Message-
From:
: Daniel Blankenberg [d...@bx.psu.edu]
Sent: Monday, October 03, 2011 2:00 PM
To: Paniagua, Eric
Cc: Nate Coraor; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
Hi Eric,
Can you provide an example of the composite datatype
?
Thanks,
Eric
From: Daniel Blankenberg [d...@bx.psu.edu]
Sent: Monday, October 03, 2011 2:00 PM
To: Paniagua, Eric
Cc: Nate Coraor; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] (Composite) Dataset Upload not Setting Metadata
Hi Eric,
Can you
Hi John,
You can do: sh run_unit_tests.sh to run these, along with the other doctests
in the core code.
Thanks for using Galaxy,
Dan
On Oct 5, 2011, at 1:17 PM, Duddy, John wrote:
There are several files in Datatypes with doctest tests in them. Is there a
convenient wrapper script to run
Hi Roy,
Have you tried setting debug=False and use_interactive=False in the
universe_wsgi.ini file?
Thanks for using Galaxy,
Dan
On Oct 5, 2011, at 2:32 PM, Glen Beane wrote:
On Oct 5, 2011, at 2:25 PM, Roy Weckiewicz wrote:
Hi,
We have a local galaxy instance running on mac osx
Hi Ilya,
The 'actions' tagset must be within the ''data' tagset, you have it outside.
Try something like:
data format=sam name=output2 label=${tool.name} on ${on_string}:Output
Sam File
actions
action type=metadata name=dbkey
option type=from_data_table
Hi Alex,
There will be an update to the GATK tools in Galaxy in the coming weeks, for
compatibility with version 1.2 of the GATK. There have been several changes
that are not directly backwards compatible, including much of the ROD handling
(which now will only accept vcf files for the most
Hi Ilya,
In addition to the ones that you mention, there is also .metadata,
.extra_files_path, .name which can be useful. The input wrapper will allow
access to any of the attributes associated with the DatasetInstance (see class
of this name in lib/galaxy/model/__init__.py), but using these
intervals menu not showing the bed
file as an option:
Thanks again,
Alex
On Oct 18, 2011, at 1:46 PM, Daniel Blankenberg wrote:
Hi Alex,
There will be an update to the GATK tools in Galaxy in the coming weeks, for
compatibility with version 1.2 of the GATK. There have
Hi Ilya,
In datatypes_conf.xml, under the bam datatype uncomment out the display
application for igv/bam (display file=igv/bam.xml /). Links will then
appear for bam history items.
Thanks for using Galaxy,
Dan
On Oct 24, 2011, at 5:50 PM, Chorny, Ilya wrote:
I saw some posts and a commit
Hi Jim,
The preferred method to add external datasources is the URL-based callback
mechanism as described in http://www.ncbi.nlm.nih.gov/pubmed/21531983 and
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources. It has proven
effective for importing data from various data resources using
Hi Ilya,
You can validate dbkeys using validators including metadata,
dataset_metadata_in_file/data_table, unspecified_build and others.
Could you clarify what GATK tools you are trying to modify and exactly what you
are trying accomplish? A complete example xml file, and any additional files
Hi Carlos,
This is a known bug with running workflows and we are working on a fix. Thanks
for reporting this error.
The current work-around is to set the reference genome value in the select
boxes (currently only 'hg_g1k_v37' is available on our public server) directly
within the workflow
Hi Ivan,
For the displays at external resources that rely on partial gets/responses
(e.g. bams, bigWig, etc), Galaxy will need to be put behind a proxy, e.g. nginx
with x_accel_redirect or apache with xsendfile. Please see the production
server instructions on the wiki for information on
Hi Carlos,
Thanks for reporting this issue. Most (but not all) of the ROD files for the
GATK now require VCF. I have updated Indel Realigner in changeset
6320:945c7a47755f to reflect this.
Thanks for using Galaxy,
Dan
On Nov 21, 2011, at 4:27 PM, Carlos Borroto wrote:
Hi,
I found that
Hi James,
Can you let us know which revision of Galaxy that you are using (hg head) and
any log output that appears when accessing or running the tool? Also the list
of parameters and values that are being POSTed to Galaxy and a copy of your
tool.xml file would be useful.
Thanks for using
:Thu Sep 29 16:45:19 2011 -0400
Thanks again,
-James
P.S. It's my pleasure to use Galaxy! ;)
On Thu, Dec 1, 2011 at 7:06 AM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi James,
Can you let us know which revision of Galaxy that you are using (hg head) and
any log
:25 AM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi James,
For legacy reasons, Biomart uses a special-cased GALAXY_URL parameter, which
is likely the source of the problem. If you remove the 'param
name=GALAXY_URL ... /' input parameter, restart Galaxy and reload the
Galaxy interface, does
Hi Susan,
Sorry for the delay in response. Are you still experiencing these problems? If
so, would you mind sharing a history and your workflow with me and I will take
a look.
Thanks for using Galaxy,
Dan
On Sep 20, 2011, at 4:28 PM, Susan Newman wrote:
I’m working on a SOLiD ChIP-Seq
Hi Amelia,
Sorry for the delay in reply. Could you provide a copy of your xml file and we
can take a look.
Thanks for using Galaxy,
Dan
On Nov 21, 2011, at 12:26 PM, Amelia Ireland wrote:
Can anyone answer this, please, or point me to the relevant documentation?
On 07/11/2011, Amelia
Hi James,
In your universe-wsgi.ini file you specify the actual list of admin users, not
a file containing the users:
# Administrative users - set this to a comma-separated list of valid Galaxy
# users (email addresses). These users will have access to the Admin section
# of the server, and
Hi Makis,
Ordinarily in interactive mode, ctrl+c should work. However, when just using
'run.sh' certain python/OS combinations experience issues. You'll need to
manually kill your instance, e.g. using 'kill pid'. Next time you start
Galaxy you can use 'run.sh --reload' which should enable
Hi Matt,
The asynchronous protocol should be working fine.
Can you confirm that your flow is similar to:
- User starts at Galaxy, gets sent to external resource with 'GALAXY_URL'
parameter.
- User browses external site and selects options, sends data to Galaxy by using
the GALAXY_URL
Hi Ming,
From Galaxy, you can currently view BAM and VCF (VCF is available in -central,
but will be in the next -dist release) files within IGV. To do this on a local
set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx
or apache); this enables byte-range requests. In
18th right?!
Thanks
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
[galaxy-dev-boun...@lists.bx.psu.edu] namens Daniel Blankenberg
[d...@bx.psu.edu]
Verzonden: dinsdag 17 januari 2012 15:09
Aan: igv-h...@googlegroups.com
CC: galaxy-dev@lists.bx.psu.edu
Hi Jim,
Yes, Galaxy ships the vcf files bgzip compressed (filename.vcf.gz) and makes a
tabix index available along side (filename.vcf.gz.tbi). In the case of Galaxy,
the pysam package is used to create the tabix index.
Thanks,
Dan
On Jan 17, 2012, at 9:44 AM, Jim Robinson wrote:
Hi Dan,
Hi Josh,
It sounds like you are really close to getting this to work. My first guess
would be that there is an issue with the modified ucsc_build_sites.txt file.
Can you check that the line you copied is tab delimited and not space delimited?
Thanks for using Galaxy,
Dan
On Feb 27, 2012, at
Hi Curt,
This is an annoyance when trying to use these tools interactively, but running
or designing a workflow in the editor should work just fine. The issue is that
for Galaxy the BAM index is technically considered an optional metadata
attribute, but it is required for GATK. I've removed
the entries, but once I did a 'set list' in vi to
display formatting characters I saw that 'main' had the tab ^I characters but
my 'internalgb' entry didn't. This must have happened because I did a visual
copy with my cursor. Thank you.
-Josh
On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg d
Hi Jim,
Admin only actions are accessed from under the Admin panel. Can you check that
you are accessing the Library from under the Admin interface and not from under
Shared Data?
Thanks for using Galaxy,
Dan
On Feb 27, 2012, at 12:24 PM, James Vincent wrote:
Hello,
I have been upload
Hi Curt,
This should be fixed in -central (https://bitbucket.org/galaxy/galaxy-central)
in changeset 6778:35be930b21be and will be available in the next dist release.
If you don't want to wait until the next dist release, you can also pull
directly from central or apply the changes manually.
Hi Vidya,
It appears that the SICER shell scripts are not available on the path of the
user that Galaxy is running under: An error occurred running this job:
/bin/sh: SICER-rb.sh: not found. Make sure that the scripts from the SICER
package are available on the path and that they are
Hi Brad,
I just ran the updateucsc.sh script and it seemed to work correctly. Can you be
more specific as to which builds you are missing and could you try running the
script again and if it doesn't work, copy the log output here?
Thanks for using Galaxy,
Dan
On Mar 6, 2012, at 12:15 PM,
Hi Vidya,
SICER is currently restricted to 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3',
'sacCer1', 'pombe', 'rn4', 'tair8' dbkeys. The issue here is that SICER itself
has the needed chromosome length information hard coded. I wrote to the authors
last year suggesting a simple way to avoid
Hi Hanfei,
I would strongly suggest against having an input field for a password in a
Tool, it is not secure at all.
Also, as an FYI, we're working locally on GenomeSpace interoperability
functionality and it should be released relatively soon, so you may want to
hold off on your efforts for
Hi Mark,
Try these changes:
tool id=sra-trace-download name=Download SRA data tool_type=data_source
and
param name=GALAXY_URL type=baseurl
value=/tool_runner?tool_id=sra-trace-download/
Although 'GALAXY_URL' should be generated automatically if it is not included
explicitly for
Hi Lisa,
The implicit conversion of your BED file to a GeneTrack file failed. The usual
cause for this is a missing dependency such as tables or hdf5. Running the
converter in a standalone mode (click on the pencil icon for the bed dataset
and look for 'convert') should give some more
Hi Aaron,
If you are designing a new datatype for a (set of) tool(s) and this datatype
requires a bunch of files to be in a directory and these files are generally
only useful when they are bundled together as a single unit (i.e. you wouldn't
normally want any one of the files to exist as a
Hi Rob,
At this time, these tools are still included within the main Galaxy
distribution under tools/gatk. I would recommend using the latest version
available from galaxy-central until they are migrated into the toolshed.
Please let us know if you encounter any issues.
Thanks for using
Hi Ira,
You'll want to set this up as a dynamic display application, where the link id,
name, url, port, etc are defined in an external tab-delimited file. Most of the
displays included in the dist are set up this way, one example would be the
display_applications/ucsc/bam.xml.
For an
Hi Raja,
Can you check that your fields are tab separated and not spaces (they are
spaces below, but that could be a copy and paste artifact)?
Thanks for using Galaxy,
Dan
On May 9, 2012, at 9:45 AM, Raja Kelkar wrote:
Hi Jen,
Thank you for your response. I seem to have all the
Hi Rob,
Changeset 7300:f197c4346cc4, which is currently available in galaxy-central,
should allow the external display applications to work when require_login =
True, thanks for reporting this error. Please let us know if you encounter
additional issues.
Thanks for using Galaxy,
Dan
On
On Sat, Jun 23, 2012 at 1:32 AM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Rob,
Changeset 7300:f197c4346cc4, which is currently available in galaxy-central,
should allow the external display applications to work when require_login =
True, thanks for reporting this error. Please let us
Hi Rob,
The 'bed' datatype in Galaxy refers to UCSC's Browser Extensible Data format
(http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
Is this a binary PLINK .bed file
(http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml)? If so, you may want
to consider looking at/using the 'pbed'
Hi Sascha and Geert,
A quick and dirty way to get the API key during tool execution would be
something like:
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
Of course, it would be better if there were a more straightforward way to
access the key. It would also be a good idea to add
Hi David and Bastal,
We have been able to reproduce this behavior under certain conditions and are
working on a fix. Until this fix is available, you can disable ajax uploads,
which should allow the upload tool to work properly.
In tools/data_source/upload.xml change
param name=file_data
using the FreeBayes tool in our local Galaxy instance for some
time. As FreeBayes is a rapidly evolving tool, it has been very helpful to
have Daniel Blankenberg work on keeping an updated wrapper.
Recently, I've run into a rather troublesome bug in FreeBayes
(https://github.com/ekg/freebayes
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 they are recognized? Or am I
missing something?
Lance
Daniel Blankenberg wrote:
Hi Lance,
Thank you
Hi Lance,
Thank you for finding this issue and a bigger thanks for the patch. We've
updated FreeBayes in the toolshed with your patch. Please let us know if you
encounter further issues.
Thanks!
Dan
On Sep 11, 2012, at 5:08 PM, Lance Parsons wrote:
Today I ran into a new issues with
Hi Felix,
Thanks for reporting this error, it has been fixed in revision
7663:cc064ff4249b. Please let us know if you encounter additional issues.
Thanks for using Galaxy,
Dan
On Sep 10, 2012, at 12:23 PM, Felix Homa wrote:
Hello,
We noticed a problem with the tool Filter Fastq. It
Hi Liisa and Peter,
There was an issue if your workflows were created using the ncbi blast tools
from the distribution (e.g. versions 0.0.11) and you only had installed the
latest tools from the toolshed (e.g. versions 0.0.13). This has been corrected
in changesets 7754:371f6770d25c through
Hi Brad,
Thanks for reporting this error, it has been fixed in changeset
7902:2d12f10c87c7 and will be available in the next distribution.
Thanks for using Galaxy,
Dan
On Oct 13, 2012, at 10:30 PM, Langhorst, Brad wrote:
Error - type 'exceptions.NameError': global name 'string' is not
Hi Alex,
Thanks for reporting this error. This is likely caused by the change in type
for one of the parameters used in the tool between when the original job was
run and when the workflow extraction was attempted. I've committed a fix in
changeset 8169:6ff28399645a and also added a warning
Hi Peter,
Excellent suggestion. I've replaced the outdated hard-coded minimum version
check in set_metadata.py with a call to check_python() in changeset
8171:4b62ed46e5b6. As you note, there are likely other scripts that could
benefit from a similar change; patches and pull requests are
Hi Joachim,
It looks like your integrated_tool_panel.xml file has been corrupted somehow.
You can move this file to a backup location (or delete) and it should be
automatically regenerated on Galaxy startup. If this fixes the issue, could you
share a copy of the file? It might be helpful for
you told me and now I can't start galaxy it tells me Galaxy deamon not
running,please help
Sent from my Verizon Wireless BlackBerry
From: Daniel Blankenberg d...@bx.psu.edu
Date: Tue, 13 Nov 2012 10:10:43 -0500
To: Rolando Mantillarolandomantil...@gmail.com
Cc: galaxy-u...@lists.bx.psu.edu
Hi Samuel,
You can import and use the restore_text function from galaxy.lib.util to
restore the characters.
Alternatively, you may want to look at customizing the sanitizer you are using
for the tool input, e.g. only sanitize the quote character that you are using
around the command-line
Minor correction for the import, you could do:
from galaxy.util import restore_text
in a tool executed from Galaxy.
On Nov 16, 2012, at 2:50 PM, Daniel Blankenberg wrote:
Hi Samuel,
You can import and use the restore_text function from galaxy.lib.util to
restore the characters
Hi Joan,
For IGV and most external displays that work on BAM and other larger seekable
file formats (bigwig, bigbed, etc.) you'll need to use and configure a proxy
server for your local Galaxy instance that provides byte-range request
capabilities, such as nginx
Hi Sarah,
This looks to be due to a non-unicode character in the dataset's info field.
Are you using a Galaxy revision = 7563:fca4e12478d6?
Thanks for using Galaxy,
Dan
On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote:
Hello,
One of my users gets the following message when he wishes to
Hi Brad,
Thanks for reporting this issue. I've committed what I hope is a fix for your
issue in changeset 8527:eb4dac39eed5 in galaxy-central. Once you are able to
apply these changes, would you mind letting us know if this resolves your
broken workflows?
Thanks for using Galaxy,
Dan
On
/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py',
line 444 in value_from_basic
current_case = rval['__current_case__'] = value['__current_case__']
TypeError: 'NoneType' object is unsubscriptable
Brad
On Jan 7, 2013, at 11:21 AM, Daniel Blankenberg d...@bx.psu.edu
Hi Liisa,
Thank you for reporting this bug. A fix has been committed
(https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed830b4f91df79b971c5)
and will be available in an upcoming release. Please let us know if you
encounter additional issues.
Thanks for using Galaxy,
Hi Thon,
The test option runs the upgrade and downgrade of the latest migration script.
I'm assuming that you had already run the latest migrations available and the
server was up and running OK (other than the dataset size issue) before trying
the test command.
On a COPY of your database,
Hi Oya,
This is the link: http://wiki.galaxyproject.org/MailingLists
Thanks for using Galaxy,
Dan
On Feb 20, 2013, at 8:39 AM, Dannon Baker wrote:
Hi Oya,
Here's a wiki page detailing how to subscribe and unsubscribe from any
of the galaxy mailing lists:
-Dannon
2013/2/14 Oya
Hi Nicola,
Thanks again for reporting this error. This has been fixed in stable.
Thanks for using Galaxy,
Dan
galaxy-central$ hg head
changeset: 8914:31b09605fcc3
branch: stable
tag: tip
parent: 8908:a0741e6798f2
user:Daniel Blankenberg d...@bx.psu.edu
date
?
Thanks for using Galaxy,
Dan
On Feb 22, 2013, at 10:33 AM, Marc Logghe wrote:
Hi Daniel,
Thanks for the answer.
In my hands it does not work unfortunately but I’m a total python dummy.
Marc
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Friday, February 22, 2013 4:10 PM
Hi Marc,
You can force the metadata detection to search your entire file by adding a new
set_meta method to your datatype class, e.g. (untested):
def set_meta( self, *args, **kwd ):
kwd['max_data_lines'] = None
kwd['max_guess_type_data_lines'] = None
return super(
Hi Brad,
Thanks for reporting this issue. It has been fixed in -central and will be
available in the next stable release:
https://bitbucket.org/galaxy/galaxy-central/commits/b9afd514145740b4d5999158d51bd7dc4a409a99
Thanks for using Galaxy,
Dan
On Mar 15, 2013, at 5:04 PM, Langhorst, Brad
Hi Julien,
This was fixed in changeset 6cd4058d7b32
(https://bitbucket.org/galaxy/galaxy-dist/commits/6cd4058d7b32/). Can you
update your Galaxy instance and see if the issue is resolved for you?
Thanks for using Galaxy,
Dan
On Mar 20, 2013, at 4:53 AM, Julien SEILER wrote:
Hello Carl,
= p_text.replace(rematch, 'span style=background-color:%s
class=wfpspan wf_parm__%s%s/span' % (wf_parms[rematch[2:-1]],
rematch[2:-1], rematch[2:-1]))
KeyError: 'min_insert'
I'll hack a bit on it to see why min_insert is not in wf_params...
Brad
On Mar 15, 2013, at 5:28 PM, Daniel Blankenberg
Hi Vipin,
Thank you for reporting this issue.
This has to do with the way that the old-style (hard-coded) display
applications were modified after introduction of roles to authorize access to
an user's datasets that might be permission protected.
Ideally, with these old-style applications,
Hi Peter,
What is the test error given when you do have a value defined for name in
output?
Can you try using 'empty_file.dat'?
e.g.
output name=out_file file=empty_file.dat
or
output name=out_file file=empty_file.dat compare=contains
etc
Thanks for using Galaxy,
Dan
Hi Iry,
Did you align against the same reference genome that you are trying to use in
FreeBayes?
Can you copy and paste the SAM header of your BAM file? e.g. samtools view -H
file.bam
Thanks for using Galaxy,
Dan
On May 1, 2013, at 1:43 PM, Iry Witham wrote:
I uploaded the bam file to
Hi Ramon,
I've committed a patch to the stable branch that should resolve this issue.
Please update your Galaxy instance and let us know if this has fixed it for you.
Thanks for using Galaxy,
Dan
On May 9, 2013, at 8:40 AM, Ramon Tiburski wrote:
Hi,
I uploaded some data and when I
Assuming you checked Galaxy out using mercurial, stop your Galaxy instance and
go into the Galaxy root directory and execute:
hg pull -u
Then start your Galaxy instance back up.
On May 9, 2013, at 12:36 PM, Ramon Tiburski wrote:
OK. thank you so much, but how can I update my instance?
Hi Monica,
I've pushed a fix to our stable branch that should resolve this issue for you.
It will be available on our main server the next time it is updated.
For now, you should be able to work around the error by going into your stored
workflows and remove any non-ASCII characters from the
Hi Daniel,
This should work fine. You'll need to make sure that you have the host setting
in your universe_wsgi.ini like:
host = 0.0.0.0
and that the port 8080 is open/accessible in the security group settings for
the instance in AWS.
Thanks for using Galaxy,
Dan
On Jun 10, 2013, at 4:42
Hi Huayan,
Your external website should accept a parameter GALAXY_URL and use this value
as e.g. the content of the form action=xxx attribute (use a sensible
default when not starting at Galaxy and this value is not provided). Your
webpage should post back to GALAXY_URL with a parameter named
Hi Graham,
Which revision of Galaxy are you currently using? Currently data managers
require at least 9952:a28faa6ac188 on the default branch.
When installed from the tool shed, data managers use the
shed_tool_data_table_conf.xml file, could you check the contents of that file?
Also can you
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