Hi Bruno,
You may be able to get it to work if you directly specify the tool_shed.ini
file that you want to use and also provide the entire toolshed url including
protocol, e.g:
TOOL_SHED_CONFIG_FILE=path/to/tool_shed.ini sh run_tool_shed.sh
-bootstrap_from_tool_shed https://testtoolshed.g2.bx
Hi Jorrit,
Are you subclassing your tsv datatypes from tabular?
If you can post your tool xml and datatype_conf.xml additions then we should be
to provide more assistance.
Thanks for using Galaxy,
Dan
On Nov 7, 2014, at 12:27 PM, Jorrit Boekel wrote:
> Dear list,
>
> I tried to make a to
7;unicode' object has no attribute 'value'
>
> I've tried to change the param_attribute to "ext", "dbkey" (ones that
> I know that exist) and got a similar error.
>
> Bests,
> Nikos
>
> On 15 October 2014 16:58, Daniel Blankenberg
Hi Nikos,
In the very least, you’ll want to make sure that you have a bounding
tag set around your actions. It is probably also advisable
to add a set of conditional/whens around the action, since you’re only setting
the dbkey under certain circumstances.
Thanks for using Galaxy,
Dan
On O
First guess is that perhaps the system is still defaulting to using java 1.6
and not 1.7. What happens if you run “java -version” as the Galaxy system user?
Perhaps try a reboot of the vm as well to make sure that the Galaxy app is
running with java 1.7.
Also, is this a custom vm? If it using
> d.
>
> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre
> for Disease Control
> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
>
> From: Daniel Blankenberg [d...@bx.psu.edu]
> Sent: Frida
Hi Damion,
Text fields are not currently able to be populated by dynamic_options, but in a
dynamic_options select list you could access the user’s username directly. If
you want the user to be able to override it, you could have a conditionally
used empty text box that your tool defaults to usi
Hi Melissa,
It is possible to do things like this using dynamic_options and a code file,
which are somewhat deprecated, but still usable. An example that you might want
to look at could be the GenomeSpace Export tool
(tools/genomespace/genomespace_exporter.*), which queries the GenomeSpace API
Hi Iry,
First thing to check is that your fields are tab delimited — they appear to be
spaces instead of tabs in this email, but copy and pasting into email can munge
things sometimes (also “gh19.fa” is probably a typo, but that wouldn’t prevent
the selection option from showing up).
Thanks f
Hi Graeme,
It looks like your integrated_tool_panel.xml file has been corrupted. You can
move/remove this file and it will be recreated the next time Galaxy is started
up.
Thanks for using Galaxy,
Dan
On Sep 3, 2014, at 3:54 AM, Graeme Grimes wrote:
> I have tried to restart Galaxy after
Hi Julie,
Unfortunately the builds distributed with Galaxy are hardcoded to be located
under “GALAXY_ROOT/tool-data/shared/ucsc/builds.txt”. We should probably make
this configurable/use the configured tool-data directory, however, in the mean
time, would it be possible for you to set up a sym
Slightly off topic, but I would like to caution that if you want to be able to
ensure that your workspace is still available across time periods/browser
sessions on the public site, then you should most definitely use registered
accounts, as we will not be able to recover any "lost" anonymous hi
Hi Stephen,
Can you provide the error message from the job? You can look at bug-report for
the the output dataset created by the data manager for the “Data Manager
History (automatically created)” history in your saved histories. Also any
other relevant information from the log would be great a
Hi Jun,
You should be using Tool Data Tables instead of acting on .loc files directly.
You can specify a data table to be built up from more than one file and
multiple data tables to use various file configurations.
‘from_data_table’:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Hi All,
I think it makes a lot of sense to allow disabling the addition of stderr
and/or stdout to dataset.info on a per tool/output dataset basis. I’ve added a
Trello card for this here: https://trello.com/c/hC5HABnr. Not sure when anyone
might have a chance to look into it, but pull requests
Hi Jun,
Do you also have require_login = True, set in your universe_wsgi.ini? That will
disable anonymous access.
Thanks for using Galaxy,
Dan
On May 10, 2014, at 8:44 PM, Jun Fan wrote:
> Dear all,
>
> Has anyone got the problem of enabling user account activation
> recently? In
Hi Bradley,
For your inputs, don’t use periods (‘.’) within the param names.
Thanks for using Galaxy,
Dan
On Apr 29, 2014, at 12:32 PM, Bradley Belfiore wrote:
> The XML file is:
>
> Pathview is a tool set for pathway based data integration
> and visualization. It maps and renders a wide
Hi Peter,
Looks like you are missing the -data_managers flag, try this:
run_functional_tests.sh -data_managers -id data_manager_blast_db
Let us know if you encounter more issues.
Thanks,
Dan
On Apr 11, 2014, at 12:15 PM, Peter Cock wrote:
> Hi all,
>
> I'm currently trying to manually ins
Hi Peter,
Having a standalone repository that just contained the tool data table and .loc
file that could be a dependency of other repositories would be a good way to go
here. Unfortunately, this isn’t supported right now. I’ve opened a trello card
for this: https://trello.com/c/VZxV08Qt
Howev
Hi Peter,
It would be great to have the BLAST tools use tool data tables and Data
Managers. Let me know what I can do to help.
Thanks,
Dan
On Apr 7, 2014, at 11:48 AM, Peter Cock wrote:
> Hi Daniel,
>
> Would you be OK with me/us incorporating your example
> Galaxy Data Manager [1] for NC
s a lot!
>
> Best,
>
> Xiaofei
>
> From: Wang, Xiaofei
> Sent: Wednesday, April 02, 2014 11:21 AM
> To: Daniel Blankenberg
> Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu
> Subject: RE: [galaxy-dev] snpEff and FASTQ Su
Hi Nilaksha,
You should be able to download a file of any size in your browser from Galaxy.
Can you try disabling the developer settings in your universe_wsgi.ini file and
see if that helps? Info for doing that is here:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Di
Hi Xiaofei,
To get the complete error message, can you click on the bug icon (left-most
icon at the bottom of the expanded history item) of the error’d dataset and
copy and paste from the page that loads in the middle pane?
Thanks for using Galaxy,
Dan
On Apr 2, 2014, at 12:04 PM, Wang, Xia
Hi Brian,
Have a look at purging histories and datasets:
https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
Thanks for using Galaxy,
Dan
On Mar 22, 2014, at 9:24 PM, Brian Claywell wrote:
> Is there an existing method for finding files in
> $GALAXY_DI
Hi Ravi,
To view histories shared with you, click on the history options (gear icon in
the right) and click “View Histories Shared with Me”. To view shared workflows,
go into the workflow interface and scroll down to the “Workflows shared with
you by others”. Please let us know if that doesn’t
Hi Ravi,
I checked and the bowtie2 tool repository had a misconfigured data table name
in its tool_data_table_conf.xml.sample file that was erroneously creating a
tophat2_indexes data table, whereas the tool itself uses bowtie2_indexes.
Can you try to uninstall and reinstall bowtie2 from the t
Hi Brad,
Galaxy doesn’t come with any Data Managers in the distribution, so you’ll need
to install them from a toolshed. Here is the Data Manager category with with is
currently available in the test toolshed.:
http://testtoolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=83f7
Hi all,
I just wanted to point out that there are several different ways to compare the
history output item to a test file beyond the default “diff”, including
contains, re_match, sim_size, etc, this is set by the “compare” attribute in
the xml tag for the test output. If you really don’t care
Hi Eric,
Thanks for reporting this error, it has been resolved in changeset
12278:04bce95d8fd2 and 12281:6c5913a4b701. Please let us know if you encounter
additional issues.
Thanks for using Galaxy,
Dan
On Jan 27, 2014, at 4:56 AM, Eric Kuyt wrote:
> Hi Greg or James,
>
> This morning I
Hi Greg,
The easiest way would be to actually start up the old instance via the
cloudlaunch and then terminate it while checking the box to “Also delete this
cluster?" after termination in the CloudMan interface.
Otherwise, you can manually delete the S3 bucket (this is where the listing is
pa
Hi Peter,
Please see replies inline, below.
Thanks,
Dan
On Oct 17, 2013, at 5:36 AM, Peter Cock wrote:
> Hi Dan,
>
> On Tue, Oct 15, 2013 at 7:40 PM, Daniel Blankenberg wrote:
>> Hi all,
>>
>> I think what we have are two similar, but somewhat separate problem
Hi all,
I think what we have are two similar, but somewhat separate problems:
1.) We need a way via the UI for an admin to be able to add additional
configuration entries to data tables / .loc files.
2.) We need a way to bootstrap/initialize a Galaxy installation with data
table/ .loc file entri
Hi James,
The FASTX fastq to fasta conversion tool requires your input to be in one of
the "fastqsanger,fastqsolexa,fastqillumina" datatypes. Please note that this
does not include the base "fastq" datatype. Can you double check the datatype
assigned to your datasets?
Alternatively, there is a
chr8_gl000197_random.maf.index
> -rw-rw-r-- 1 postgres postgres 13G Oct 31 2009 chr8.maf
> -rw-rw-r-- 1 postgres postgres 201M Sep 10 00:08 chr8.maf.index
> ==
>
> And thanks for the suggestion of adding an extra dir level, I will do that.
>
> At the moment, I only need prima
Hi Leon,
What is the output of "ls -lah /mnt/galaxyIndices/alignments/maf/"?
Also, you may what to use additional sub-directory structure for your file
locations in case you want to add more alignments later, e.g.,
/mnt/galaxyIndices/hg19/maf/10_way_multiz/ or similiar
Also, note that although
rted the instance, still no luck. Sorry.
>
> Thanks, Vipin
>
>
> On Fri, Aug 9, 2013 at 3:43 PM, Daniel Blankenberg wrote:
> Hi Vipin,
>
> Can you try deleting the contents of your compiled templates directory (i.e.
> /codebase/database/compiled_templates/*)?
>
der_context
> **kwargs)
> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", line 692, in
> _render_context
> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> File "/codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py", lin
Hi Vipin,
This has been fixed in the stable branch of galaxy-central
https://bitbucket.org/galaxy/galaxy-central/commits/cd6fec2f5cba but has not
made it on to galaxy-dist yet.
Thanks for using Galaxy,
Dan
On Aug 9, 2013, at 2:33 PM, Vipin TS wrote:
> Hello dev-team,
>
> I am experienci
Hey Mo,
You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to
create your instance, it should display an example connection string that will
work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem
ubuntu@IP', after your instance launched.
Once ins
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 c
Hi Huayan,
Your external website should accept a parameter "GALAXY_URL" and use this value
as e.g. the content of the 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 "URL" which
c
Hi Marco,
You'll need to enable some missing tool data tables in
tool_data_table_conf.xml. i.e. adding:
value, dbkey, name, path
value, name, gatk_value, tools_valid_for
Also make sure the files exist at the listed , they probably
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 P
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 n
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 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 cl
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 t
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.
or
etc
Thanks for using Galaxy,
Dan
On Apr 4, 2013, at 1:34 PM, Peter Cock wrote:
> On Wed, Apr 3, 2013 at 2:48 PM, Peter Cock wro
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, mu
338 in row_for_param
> return
> render_row_for_param(context,param,value,other_values,error_dict,prefix,step,already_used)
> File
> '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py',
> line 571 in render_row_for_para
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,
>
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 wr
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( Clo
your tool?
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]
&g
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
date:Thu Feb 21
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
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, you
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,
Da
Hi Peter,
As you guessed, this debug statement is not a true error and can be safely
ignored. Its part of some undocumented features (read as don't try to use it
yet). As this does seem to be causing some confusion lately, perhaps we should
remove the log.debug until after the feature is ready,
m_strings
> value = params[key].value_from_basic( value, app, ignore_errors )
> File
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py',
> line 444 in value_from_basic
> current_case = rval['__current_case__'] = value['__current_case__&#
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
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
Hi jj,
Patch applied in 8369:bd020b5aa531. Thanks for catching and submitting!
Dan
On Dec 10, 2012, at 12:27 PM, Jim Johnson wrote:
> Fix for SelectToolParameter rerun,workflow when multiple="true"
>
> The following change allows multiple select values to be set on rerun and in
> workflow
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
(http://wiki.galaxyproject.org/
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 th
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 arg
ike
> 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
> Date: Tue, 13 Nov 2012 10:10:43 -0500
> To: Rolando Mantilla
> Cc:
> Subject: Re: [galaxy-user]
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 us
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 always
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 mes
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 - : global name 'string' is not defined
> URL: http://galaxy.ne
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 775
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 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 inst
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 Blankenber
een 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
> (ht
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
to
Please let us know
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 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' data
u.be/88MKSHHYHjc for an example.
>
> Thanks for the great work, Galaxy devs.
>
> -r
>
>
> On Sat, Jun 23, 2012 at 1:32 AM, Daniel Blankenberg wrote:
> Hi Rob,
>
> Changeset 7300:f197c4346cc4, which is currently available in galaxy-central,
> should allow the ext
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 Jun
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 relev
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 example
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 Gala
Hi Sergei,
The current MACS tool that comes with Galaxy uses MACS 1.3.7.1 from
http://liulab.dfci.harvard.edu/MACS/Download.html.
Thanks for using Galaxy,
Dan
On Mar 28, 2012, at 6:38 PM, Sergei Manakov wrote:
> Hello,
>
> I am trying to set up MACS tool on local Galaxy. Galaxy comes with
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 sep
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 informati
Hi Mark,
Try these changes:
and
Although 'GALAXY_URL' should be generated automatically if it is not included
explicitly for 'data_source' tool types.
Also, make sure that your application is including a "URL" parameter in the
post back to Galaxy. Using GET requests should also work.
P
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 n
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 havin
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, La
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 configur
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 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 uplo
was exactly the same
> to the eye in vi for all 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 &q
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
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 Vidya,
One quick thing to check is that you installed MACS version 1.3 which is
supported by the wrapper and not version 1.4 which is not yet supported.
Thanks for using Galaxy,
Dan
On Jan 24, 2012, at 7:41 AM, Hans-Rudolf Hotz wrote:
>
>
>
> On 01/24/2012 06:19 AM, Vidya .H.K wrote
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,
> The latest is from November 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
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