Re: [galaxy-dev] Dynamic data library
On 10/01/2013 07:12 PM, Cole, Nathan (NIH/NCI) [C] wrote: One final question as I dive into looking at these two methods: can you expose whole hierarchies and directories using the from_file method or will this only work on an individual sample basis? yes, you can. as an example have a look at the affymetrix cel files we offer. See attachment for a screen shot and the coresponding fragment from the xml file: options option name=Affymetrix value=Affymetrix option name=HumanGeneST10_TissueData value=HumanGeneST10_TissueData option type=meta_key name=MouseTP_Brain_01_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_01_mGENE.CEL/ option type=meta_key name=MouseTP_Brain_02_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_02_mGENE.CEL/ option type=meta_key name=MouseTP_Brain_03_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Brain_03_mGENE.CEL/ option type=meta_key name=MouseTP_Embryo_01_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_01_mGENE.CEL/ option type=meta_key name=MouseTP_Embryo_02_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_02_mGENE.CEL/ option type=meta_key name=MouseTP_Embryo_03_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Embryo_03_mGENE.CEL/ option type=meta_key name=MouseTP_Heart_01_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_01_mGENE.CEL/ option type=meta_key name=MouseTP_Heart_02_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_02_mGENE.CEL/ option type=meta_key name=MouseTP_Heart_03_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Heart_03_mGENE.CEL/ option type=meta_key name=MouseTP_Kidney_01_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_01_mGENE.CEL/ option type=meta_key name=MouseTP_Kidney_02_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_02_mGENE.CEL/ option type=meta_key name=MouseTP_Kidney_03_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Kidney_03_mGENE.CEL/ // option type=meta_key name=MouseTP_Thymus_03_mGENE.CEL value=/***/***/external/Affymetrix/HumanGeneST10_TissueData/MouseTP_Thymus_03_mGENE.CEL/ /option option name=MouseGeneST10_TissueData value=MouseGeneST10_TissueData option type=meta_key name=MouseTP_Brain_01_mGENE.CEL value=/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Brain_01_mGENE.CEL/ option type=meta_key name=MouseTP_Brain_02_mGENE.CEL value=/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Brain_02_mGENE.CEL/ // option type=meta_key name=MouseTP_Thymus_03_mGENE.CEL value=/***/***/external/Affymetrix/MouseGeneST10_TissueData/MouseTP_Thymus_03_mGENE.CEL/ /option /option option name=GEO value=GEO // /option /options If not, is there any method for exposing a the whole of a directory on the file system? Thanks, Nathan -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Tuesday, October 01, 2013 10:11 AM To: Cole, Nathan (NIH/NCI) [C] Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] Dynamic data library On 10/01/2013 03:53 PM, Cole, Nathan (NIH/NCI) [C] wrote: Thank you both for your responses. I will be looking into both of these. With regard to the from_file option to add the sample selection into the tool: I assume this means that the metadata and everything is loaded into galaxy at the time the tool is run. This depends on how you write your tool. Do you just wanna read the ie fastq file or do you also wanna read the meta data. Also, how is the meta data accessible? eg. is it stored in a txt file at the same location as the fastq file? Does this create a copy of the loaded file or simply read it in place? Also are there any efficiency issues created using this method, outside of the tool run time increase due to the load of the data taking place in-tool? It should just read it in place Hans-Rudolf Thanks, Nathan -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Tuesday, October 01, 2013 4:07 AM To: Cole, Nathan (NIH/NCI) [C] Cc: Martin Čech; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Dynamic data library Hi Nathan Do you have many tools working with those samples or just a few? If you only have a limited, predefined set of tools you might wanna consider adding the sample selection into the tool. You can use the from_file, or from_data_table options to dynamically create sample selection list. You can even drill down a hierarchical list. Have a look at
[galaxy-dev] Galaxy STARTUP ERROR!
Hi!
I am trying to launch Galaxy locally but I'm getting the following error:
tkx417:galaxy pascarellagiovanni$ sh run.sh
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 374, in loadobj
global_conf=global_conf)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 399, in loadcontext
global_conf=global_conf)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 423, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 561, in get_context
section)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 620, in _context_from_explicit
value = import_string(found_expr)
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 125, in import_string
return pkg_resources.EntryPoint.parse(x= + s).load(False)
File /Users/pascarellagiovanni/Desktop/galaxy/lib/pkg_resources.py, line
1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File /Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/__init__.py,
line 4, in module
from framework import expose
File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/framework/__init__.py,
line 40, in module
from babel.support import Translations
File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/support.py,
line 29, in module
from babel.dates import format_date, format_datetime, format_time, LC_TIME
File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py,
line 34, in module
LC_TIME = default_locale('LC_TIME')
File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 642, in default_locale
return '_'.join(filter(None, parse_locale(locale)))
File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 763, in parse_locale
raise ValueError('expected only letters, got %r' % lang)
ValueError: expected only letters, got 'utf-8'
Anybody knows what this is about?
Thanks,
Giovanni
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Re: [galaxy-dev] Galaxy STARTUP ERROR!
This looks to be a bug with the version of babel we're using (fixed in a
newer revision that I'll update to after testing), combined with improperly
set environment variables. Can you check your environment (just `env` in a
terminal) and look for LC_ALL, LANGUAGE, and LANG. Are any of these set to
*just* utf-8? It looks like they should probably be in a format like
en_US.utf-8.
On Wed, Oct 2, 2013 at 5:30 AM, Giovanni Pascarella muju...@hotmail.comwrote:
Hi!
I am trying to launch Galaxy locally but I'm getting the following error:
*tkx417:galaxy pascarellagiovanni$ sh run.sh*
*Traceback (most recent call last):*
* File ./scripts/paster.py, line 33, in module*
*serve.run()*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 1049, in run*
*invoke(command, command_name, options, args[1:])*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke*
*exit_code = runner.run(args)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 220, in run*
*result = self.command()*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py,
line 643, in command*
*app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp*
*return loadobj(APP, uri, name=name, **kw)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 374, in loadobj*
*global_conf=global_conf)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 399, in loadcontext*
*global_conf=global_conf)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 423, in _loadconfig*
*return loader.get_context(object_type, name, global_conf)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 561, in get_context*
*section)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 620, in _context_from_explicit*
*value = import_string(found_expr)*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py,
line 125, in import_string*
*return pkg_resources.EntryPoint.parse(x= + s).load(False)*
* File /Users/pascarellagiovanni/Desktop/galaxy/lib/pkg_resources.py,
line 1954, in load*
*entry = __import__(self.module_name, globals(),globals(),
['__name__'])*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/__init__.py, line
4, in module*
*from framework import expose*
* File
/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/framework/__init__.py,
line 40, in module*
*from babel.support import Translations*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/support.py,
line 29, in module*
*from babel.dates import format_date, format_datetime, format_time,
LC_TIME*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py,
line 34, in module*
*LC_TIME = default_locale('LC_TIME')*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 642, in default_locale*
*return '_'.join(filter(None, parse_locale(locale)))*
* File
/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 763, in parse_locale*
*raise ValueError('expected only letters, got %r' % lang)*
*ValueError: expected only letters, got 'utf-8'*
Anybody knows what this is about?
Thanks,
Giovanni
___
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Re: [galaxy-dev] Dynamic data library
One final question as I dive into looking at these two methods: can you expose whole hierarchies and directories using the from_file method or will this only work on an individual sample basis? If not, is there any method for exposing a the whole of a directory on the file system? Thanks, Nathan -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Tuesday, October 01, 2013 10:11 AM To: Cole, Nathan (NIH/NCI) [C] Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] Dynamic data library On 10/01/2013 03:53 PM, Cole, Nathan (NIH/NCI) [C] wrote: Thank you both for your responses. I will be looking into both of these. With regard to the from_file option to add the sample selection into the tool: I assume this means that the metadata and everything is loaded into galaxy at the time the tool is run. This depends on how you write your tool. Do you just wanna read the ie fastq file or do you also wanna read the meta data. Also, how is the meta data accessible? eg. is it stored in a txt file at the same location as the fastq file? Does this create a copy of the loaded file or simply read it in place? Also are there any efficiency issues created using this method, outside of the tool run time increase due to the load of the data taking place in-tool? It should just read it in place Hans-Rudolf Thanks, Nathan -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Tuesday, October 01, 2013 4:07 AM To: Cole, Nathan (NIH/NCI) [C] Cc: Martin Čech; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Dynamic data library Hi Nathan Do you have many tools working with those samples or just a few? If you only have a limited, predefined set of tools you might wanna consider adding the sample selection into the tool. You can use the from_file, or from_data_table options to dynamically create sample selection list. You can even drill down a hierarchical list. Have a look at ~/tools/annotation_profiler/annotation_profiler.xml which uses the file ~/tool-data/annotation_profiler_options.xml All you need to do is keeping the file in sync with the directory structure of your samples directory Regards, Hans-Rudolf On 09/30/2013 09:48 PM, Martin Čech wrote: Hi Nathan, Dannon answered similar question few days ago: There's an import mechanism in libraries that'll allow you to simply link to the file on disk without copy/upload. I believe the example_watch_folder.py sample script (in the distribution) does just this via the API, if you want an example. This might be what you are looking for. Martin On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C] nathan.c...@nih.gov mailto:nathan.c...@nih.gov wrote: Hello, we’ve set up a local Galaxy instance in our genotyping and next-gen sequencing lab with local Apache LDAP (AD) integration, NFS mounts to a large NAS, and cluster integration coming. Do to the high volume of samples and staff that will be using the system, I want to set up data libraries (without copying to Galaxy). This is obviously no problem the first time, however I was wondering if there was a way to make a library, added from a system path, be dynamic so that it would stay synchronized with the underlying file structure? __ __ If a try dynamic library is not possible, is there a method for adding files to an existing library via that same system path that would not duplicate all of the original files in the data library? __ __ I did some scouring of the list and found some old unanswered questions and some things tangentially related topics, but I was unable to find a true answer or solution to my problem. Any information on how to do the tasks above or other solutions to provide the same functionality would be greatly appreciated. __ __ Thanks, Nathan __ __ ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your
[galaxy-dev] Toolshed Collaboration Issues
I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] workflow batch execution dynamic parameters
Dear all Related to my question yesterday I have another one: If I run a workflow in batch I can select pairs of files (the old fwd and rev reads fastq files) and the workflow is run however many times, depending on the number of pairs I select. Unfortunately all other parameters appear to be static, which is not ideal in my case. Specifically I am using bwa the map a large-ish number of (paired) samples to the same reference genome, while simultaneously setting read group information in the resulting sam files. So it's suboptimal to run this with a fixed SM value. Is there any way of dynamically setting the parameters? The set-at-runtime option also allows for a single parameter value, not a list. Ideally the set-at-runtime option would somehow allow me to input one parameter per file pair. Thanks very much in advance for your help. Cheers Ulf On 01/10/13 14:09, Joachim Jacob | VIB | wrote: Sorry, my answer doesn't fit your question. :-) J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 10/01/2013 03:08 PM, Joachim Jacob | VIB | wrote: Hi Ulf, What I do: 1. make a history, doing the steps you want to do on one input file 2. create a workflow of that history 3. assemble all input files in one history 4. run the workflow and select the multiple input files to run the workflow on. 5. Optionally: send the results to a new history, for every input file you will get a new history, properly named. Hope this helps, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 10/01/2013 02:27 PM, Ulf Schaefer wrote: Dear all We frequently find ourselves in situations where a tool needs to be run with a lot of input files. For example, run the GATK UnifiedGenotyper with easily dozens of bam files. Using the repeat in this case requires quite a bit of clicking. Is there a more conventient way fo doing this? Maybe similar to the multi-file-select that is possible for workflow inputs? I saw some older discussions on this or similar issues, but I am a bit lost what the current official stable proposed solution for this is. Thanks for your help Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tabular data not displaying in main panel
Hi all,
Multiple users of our internal Galaxy server have reported with
multiple browsers that tabular data is not displayed in the main
central panel. The preview in the history works, but clicking on
the eye icon gives a blank page.
I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML
for the central frame looks blank but is actually a script when
viewed via the frame source. The tabular file data is there in
the script's first_data_chunk entry - but does not get shown.
An except is shown below.
Has anyone else noticed this problem? I believe it began
when I last updated this Galaxy instance, but was not
noticed immediately.
Thanks,
Peter
---
I believe we are running the current stable release, or at least
the latest commit on the default branch from galaxy-dist
$ hg pull
warning: bitbucket.org certificate with fingerprint
24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not
verified (check hostfingerprints or web.cacerts config setting)
real URL is https://bitbucket.org/galaxy/galaxy-dist
pulling from http://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found
$ hg update
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
$ hg branch
default
[galaxy@ppserver galaxy-dist]$ hg log -b default | head
changeset: 10411:c42567f43aa7
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
changeset: 10410:e9ee9c5d30ae
user:Dave Bouvier d...@bx.psu.edu
date:Mon Aug 19 13:08:45 2013 -0400
summary: Remove duplicate method from the install and test's
functional_tests.py.
...
---
!DOCTYPE HTML
html
!--base.mako--
head
titleDataset Display/title
meta http-equiv=Content-Type content=text/html; charset=utf-8 /
link href=/galaxy/static/style/base.css?v=1380731103
media=screen rel=Stylesheet type=text/css /
script src=/galaxy/static/scripts/libs/jquery/jquery.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/jquery/jquery.migrate.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/jquery/select2.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/bootstrap.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/underscore.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/backbone/backbone.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/backbone/backbone-relational.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/handlebars.runtime.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/galaxy.base.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/mvc/ui.js?v=1380731103
type=text/javascript/script
script type=text/javascript
// console protection
window.console = window.console || {
log : function(){},
debug : function(){},
info: function(){},
warn: function(){},
error : function(){},
assert : function(){}
};
// Set up needed paths.
var galaxy_paths = new GalaxyPaths({
root_path: '/galaxy/',
image_path: '/galaxy/static/images'
});
/script
script src=/galaxy/static/scripts/libs/require.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/templates/compiled/helpers-common-templates.js?v=1380731103
type=text/javascript/script
script type=text/javascript
require.config({
baseUrl: /galaxy/static/scripts,
shim: {
libs/backbone/backbone: { exports: Backbone },
libs/backbone/backbone-relational: [libs/backbone/backbone]
}
});
require(['mvc/data'], function(data) {
data.createTabularDatasetChunkedView(
_.extend( {misc_blurb: 7,891 lines, peek:
table cellspacing=\0\
cellpadding=\3\trth1/thth2/thth3/th/trtrtdGpa_EST_02_04___C05_022/tdtdGO:0005737/tdtd.../td/tr/table,
data_type: tabular, deleted: false, history_id:
cdbf837ba6516a14, metadata_column_names: null, visible: true,
genome_build: ?, hid: 10, file_size: 509095,
metadata_data_lines: 7891, file_ext: tabular, id:
0ddcd2cf2375e24a, misc_info: \nBLASTX output identified\nInput
has 4507 queries\nDone\nStandard out:\nBlast2GO Pipeline Version
2.5.0\n--\n\nHash for resource
ec2go_19072011.txt of type ec created. 4003 associations
loaded.\nBlast2GO build: 23092011\nChange , hda_ldda:
[galaxy-dev] Slice bam
It seems like Slice_bam should be pretty straight-forward to use, but when I run it and give it a bed file that contains the human chromosomes with their lengths like this: chr11 249250621 chr21 243199373 for all chromosomes 1-22, X, Y. I don't get the reads on chr1 and 2; instead, all I am left with are the reads on the nonstandard chromosomes (the unmapped scaffolds). Any idea what I am doing wrong? Jean Jasinski ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed Collaboration Issues
Hi Lance, I worked for me the last time. I usually create a repository under the IUC account and add me as contributor. No problem so far. Cheers, Bjoern I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed Collaboration Issues
Perhaps it has something to do with a specific account? The user 'nilesh' tried to add me to his rseqc repository (http://toolshed.g2.bx.psu.edu/view/nilesh/rseqc ) and got a Server Error. I then created the rseqc_dev3 repository (http://testtoolshed.g2.bx.psu.edu/view/lparsons/rseqc_dev3 )on the testtoolshed and tried to add him (nilesh) and got the error indicated below. Any help in tracking this down would be appreciated. Björn Grüning wrote: Hi Lance, I worked for me the last time. I usually create a repository under the IUC account and add me as contributor. No problem so far. Cheers, Bjoern I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tabular data not displaying in main panel
Hi Peter,
we can confirm. Latest Galaxy stable version and its occurring randomly.
I was not able to reproduce it by myself.
Cheers,
Bjoern
Hi all,
Multiple users of our internal Galaxy server have reported with
multiple browsers that tabular data is not displayed in the main
central panel. The preview in the history works, but clicking on
the eye icon gives a blank page.
I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML
for the central frame looks blank but is actually a script when
viewed via the frame source. The tabular file data is there in
the script's first_data_chunk entry - but does not get shown.
An except is shown below.
Has anyone else noticed this problem? I believe it began
when I last updated this Galaxy instance, but was not
noticed immediately.
Thanks,
Peter
---
I believe we are running the current stable release, or at least
the latest commit on the default branch from galaxy-dist
$ hg pull
warning: bitbucket.org certificate with fingerprint
24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not
verified (check hostfingerprints or web.cacerts config setting)
real URL is https://bitbucket.org/galaxy/galaxy-dist
pulling from http://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found
$ hg update
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
$ hg branch
default
[galaxy@ppserver galaxy-dist]$ hg log -b default | head
changeset: 10411:c42567f43aa7
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
changeset: 10410:e9ee9c5d30ae
user:Dave Bouvier d...@bx.psu.edu
date:Mon Aug 19 13:08:45 2013 -0400
summary: Remove duplicate method from the install and test's
functional_tests.py.
...
---
!DOCTYPE HTML
html
!--base.mako--
head
titleDataset Display/title
meta http-equiv=Content-Type content=text/html; charset=utf-8 /
link href=/galaxy/static/style/base.css?v=1380731103
media=screen rel=Stylesheet type=text/css /
script src=/galaxy/static/scripts/libs/jquery/jquery.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/jquery/jquery.migrate.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/jquery/select2.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/bootstrap.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/underscore.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/backbone/backbone.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/backbone/backbone-relational.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/handlebars.runtime.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/galaxy.base.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/mvc/ui.js?v=1380731103
type=text/javascript/script
script type=text/javascript
// console protection
window.console = window.console || {
log : function(){},
debug : function(){},
info: function(){},
warn: function(){},
error : function(){},
assert : function(){}
};
// Set up needed paths.
var galaxy_paths = new GalaxyPaths({
root_path: '/galaxy/',
image_path: '/galaxy/static/images'
});
/script
script src=/galaxy/static/scripts/libs/require.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/templates/compiled/helpers-common-templates.js?v=1380731103
type=text/javascript/script
script type=text/javascript
require.config({
baseUrl: /galaxy/static/scripts,
shim: {
libs/backbone/backbone: { exports: Backbone },
libs/backbone/backbone-relational:
[libs/backbone/backbone]
}
});
require(['mvc/data'], function(data) {
data.createTabularDatasetChunkedView(
_.extend( {misc_blurb: 7,891 lines, peek:
table cellspacing=\0\
cellpadding=\3\trth1/thth2/thth3/th/trtrtdGpa_EST_02_04___C05_022/tdtdGO:0005737/tdtd.../td/tr/table,
data_type: tabular, deleted: false, history_id:
cdbf837ba6516a14, metadata_column_names: null, visible: true,
genome_build: ?, hid: 10, file_size: 509095,
metadata_data_lines: 7891, file_ext: tabular, id:
0ddcd2cf2375e24a,
Re: [galaxy-dev] Tabular data not displaying in main panel
Hi Peter,
Does the Javascript console of the browser show any error messages?
Thanks,
Sam
On Wed, Oct 2, 2013 at 2:48 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter,
we can confirm. Latest Galaxy stable version and its occurring randomly.
I was not able to reproduce it by myself.
Cheers,
Bjoern
Hi all,
Multiple users of our internal Galaxy server have reported with
multiple browsers that tabular data is not displayed in the main
central panel. The preview in the history works, but clicking on
the eye icon gives a blank page.
I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML
for the central frame looks blank but is actually a script when
viewed via the frame source. The tabular file data is there in
the script's first_data_chunk entry - but does not get shown.
An except is shown below.
Has anyone else noticed this problem? I believe it began
when I last updated this Galaxy instance, but was not
noticed immediately.
Thanks,
Peter
---
I believe we are running the current stable release, or at least
the latest commit on the default branch from galaxy-dist
$ hg pull
warning: bitbucket.org certificate with fingerprint
24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not
verified (check hostfingerprints or web.cacerts config setting)
real URL is https://bitbucket.org/galaxy/galaxy-dist
pulling from http://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found
$ hg update
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
$ hg branch
default
[galaxy@ppserver galaxy-dist]$ hg log -b default | head
changeset: 10411:c42567f43aa7
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
changeset: 10410:e9ee9c5d30ae
user:Dave Bouvier d...@bx.psu.edu
date:Mon Aug 19 13:08:45 2013 -0400
summary: Remove duplicate method from the install and test's
functional_tests.py.
...
---
!DOCTYPE HTML
html
!--base.mako--
head
titleDataset Display/title
meta http-equiv=Content-Type content=text/html;
charset=utf-8 /
link href=/galaxy/static/style/base.css?v=1380731103
media=screen rel=Stylesheet type=text/css /
script
src=/galaxy/static/scripts/libs/jquery/jquery.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/jquery/jquery.migrate.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/jquery/select2.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/bootstrap.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/libs/underscore.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/backbone/backbone.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/backbone/backbone-relational.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/libs/handlebars.runtime.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/galaxy.base.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1380731103
type=text/javascript/script
script src=/galaxy/static/scripts/mvc/ui.js?v=1380731103
type=text/javascript/script
script type=text/javascript
// console protection
window.console = window.console || {
log : function(){},
debug : function(){},
info: function(){},
warn: function(){},
error : function(){},
assert : function(){}
};
// Set up needed paths.
var galaxy_paths = new GalaxyPaths({
root_path: '/galaxy/',
image_path: '/galaxy/static/images'
});
/script
script src=/galaxy/static/scripts/libs/require.js?v=1380731103
type=text/javascript/script
script
src=/galaxy/static/scripts/templates/compiled/helpers-common-templates.js?v=1380731103
type=text/javascript/script
script type=text/javascript
require.config({
baseUrl: /galaxy/static/scripts,
shim: {
libs/backbone/backbone: { exports: Backbone },
libs/backbone/backbone-relational:
[libs/backbone/backbone]
}
});
require(['mvc/data'], function(data) {
data.createTabularDatasetChunkedView(
_.extend( {misc_blurb: 7,891 lines, peek:
table cellspacing=\0\
Re: [galaxy-dev] Toolshed Collaboration Issues
Hi, I added you successfully to: http://testtoolshed.g2.bx.psu.edu/view/bgruening/precommit_test please keep in mind that you need to remove the 'select one' button before you click submit, that is not intuitive but a known bug. Cheers, Bjoern Perhaps it has something to do with a specific account? The user 'nilesh' tried to add me to his rseqc repository (http://toolshed.g2.bx.psu.edu/view/nilesh/rseqc ) and got a Server Error. I then created the rseqc_dev3 repository (http://testtoolshed.g2.bx.psu.edu/view/lparsons/rseqc_dev3 ) on the testtoolshed and tried to add him (nilesh) and got the error indicated below. Any help in tracking this down would be appreciated. Björn Grüning wrote: Hi Lance, I worked for me the last time. I usually create a repository under the IUC account and add me as contributor. No problem so far. Cheers, Bjoern I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9 File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] URL problem
Alper, Did you problem get resolved already? Maybe on the galaxy-...@bx.psu.edu mailing list? I am posting it there in case it is still open. Please reply to let us know your current status. Please drop galaxy-u...@bx.psu.edu from the to/cc on reply and future posts to this thread. Thanks and sorry if this one got missed, Jen Galaxy team On 8/26/13 10:43 AM, Kucukural, Alper wrote: Hi, I have a problem in galaxy to get host/domain name in two different pages. First one is in the tool installation from toolshed, I got the error below, # Not Found The requested URL /admin_toolshed/prepare_for_install was not found on this server. # The second one is in the saved histories. When I click the buttons of the saved histories. I got the similar error like below. # Not Found The requested URL /history/list was not found on this server. # I haven't seen these any other pages yet. My installation is working on LDAP authentication with Proxy. So, I could not find a place to set the domain or host name in these two places that they can actually find the requested URLs. In the paster.log file. I don't get any error when I install a tool or go to another history. It doesn't report any error. Thanks for your help, Alper Kucukural ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] URL problem
Yes it is solved thanks Sent from my iPhone On Oct 2, 2013, at 6:14 PM, Jennifer Jackson j...@bx.psu.edu wrote: Alper, Did you problem get resolved already? Maybe on the galaxy-...@bx.psu.edu mailing list? I am posting it there in case it is still open. Please reply to let us know your current status. Please drop galaxy-u...@bx.psu.edu from the to/cc on reply and future posts to this thread. Thanks and sorry if this one got missed, Jen Galaxy team On 8/26/13 10:43 AM, Kucukural, Alper wrote: Hi, I have a problem in galaxy to get host/domain name in two different pages. First one is in the tool installation from toolshed, I got the error below, # Not Found The requested URL /admin_toolshed/prepare_for_install was not found on this server. # The second one is in the saved histories. When I click the buttons of the saved histories. I got the similar error like below. # Not Found The requested URL /history/list was not found on this server. # I haven't seen these any other pages yet. My installation is working on LDAP authentication with Proxy. So, I could not find a place to set the domain or host name in these two places that they can actually find the requested URLs. In the paster.log file. I don't get any error when I install a tool or go to another history. It doesn't report any error. Thanks for your help, Alper Kucukural ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Please save these dates! GCC2014: June 30 - July 2
Hello all, The 2014 Galaxy Community Conference (GCC2014)http://wiki.galaxyproject.org/Events/GCC2014 has been scheduled for June 30 through July 2, at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/ of Johns Hopkins University http://jhu.edu/, in Baltimore, Marylandhttp://visitors.baltimorecity.gov/, United States. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference will also includes a*Training Day* offering in-depth topic coverage, across several concurrent sessions. See the GCC2013 web sitehttp://wiki.galaxyproject.org/Events/GCC2013 for an idea of what happens at a Galaxy Community Conference. See you next summer, GCC2014 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2014/Organizers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
