Re: [galaxy-dev] Multiple select input error after update
Hi Alexandre, the commit seems to be also in galaxy-dist now. Anyway, this command should do the trick: hg pull -b stable https://bitbucket.org/galaxy/galaxy-central I'd suggest you to use directly the stable branch of galaxy-central, which usually gets the hotfixes much faster than galaxy-dist. But that's just my personal opinion. Best, Nicola Il 15.01.2015 17:32 Alexandre Defelicibus ha scritto: Hi Daniel, Thanks for the answer. How can I update my Galaxy instance with this fix? The fix is on galaxy-central repository and I've cloned the galaxy-dist repository. Thanks a lot, Alexandre 2015-01-14 18:29 GMT-02:00 Daniel Blankenberg : Hi Alexandre, Thanks for reporting this issue. We have committed a fix here https://bitbucket.org/galaxy/galaxy-central/commits/7fd6061e43d5/ [3] and it will be applied to additional releases soon. Please let know if you encounter additional issues. Thanks for using Galaxy, Dan On Jan 14, 2015, at 1:40 PM, Alexandre Defelicibus wrote: Hi all, I've updated a Galaxy server with the latest stable distribution latest_2015.01.13 and now a I got an error: cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file The tool has a multiple select field: On the job details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow: python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [, , , ] The command on XML is: dominance_ranking.py -i $input_pdbs This tool was working fine before the update. Any ideas what Is going wrong? Thanks a lot, Alexandre -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP ___ 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: https://lists.galaxyproject.org/ [1] To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ [2] -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP -- Nicola Soranzo http://nsoranzo.altervista.org La mia chiave PGP: http://nsoranzo.altervista.org/key.asc Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Manually adding new tools from toolshed
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes. Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool. So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct. Ryan ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Multiple select input error after update
Hi Daniel, Thanks for the answer. How can I update my Galaxy instance with this fix? The fix is on galaxy-central repository and I've cloned the galaxy-dist repository. Thanks a lot, Alexandre 2015-01-14 18:29 GMT-02:00 Daniel Blankenberg d...@bx.psu.edu: Hi Alexandre, Thanks for reporting this issue. We have committed a fix here https://bitbucket.org/galaxy/galaxy-central/commits/7fd6061e43d5/ and it will be applied to additional releases soon. Please let know if you encounter additional issues. Thanks for using Galaxy, Dan On Jan 14, 2015, at 1:40 PM, Alexandre Defelicibus adefelici...@gmail.com wrote: Hi all, I've updated a Galaxy server with the latest stable distribution latest_2015.01.13 and now a I got an error: cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file The tool has a multiple select field: param name=input_pdbs type=data multiple=true format=pdb label=PDB Files / On the job details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow: python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653290, galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653bd0, galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653d90, galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a61de10] The command on XML is: command interpreter=python dominance_ranking.py -i $input_pdbs /command This tool was working fine before the update. Any ideas what Is going wrong? Thanks a lot, Alexandre -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy-central and nginx
I thought the difference may be in the -central config handling that didn’t work with my universe_wsgi anymore or something. Will be hard to trace so I will leave this for now. I'll mail you more about the collections though, probably tomorrow. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 15 Jan 2015, at 16:27, John Chilton jmchil...@gmail.com wrote: On Fri, Jan 9, 2015 at 10:42 AM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Hi all, I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out dataset collections. First thing I run into is that things don’t seem to run well when running it on a VM (port forwarded) with nginx. If I click on tools I get a white screen instead of tool options, and the log show an error from lib/galaxy/webapps/galaxy/api/tools.py : Checking parameter file failed. The setup: URL would be galaxydomain.com:3030, which the VM manager forwards to port 80 on the galaxy VM, which there nginx would forward to port 8080. Now, my nginx is set up to work with older galaxy versions, I don’t know if that matters. I haven’t changed any config files at all yet. When I turn off nginx and serve directly on port 80 (using sudo), things look like they work. At least the tools look like they should. Has the nginx config to use changed recently or is this some weird artefact? Anyone else seen it? Since I’m just goofing around to see how collections work, it is not the end of the world for me, and I know galaxy-dist is the stable one, but still. I have not seen this and haven't heard of anyone else - it probably doesn't have anything to do with -central versus -stable though - I don't think I have seen any changes related to this recently. Are you sure you have setup all the same configuration options in your new Galaxy instance (e.g. nginx_x_archive_files_base, nginx_x_accel_redirect_base, nginx_upload_store, nginx_upload_path, remote_user, etc...)? Also do you have the same number of web threads and handler threads or both instances - if you configured you older instance to use multiple processes your new instance will need to be configured to do this as well. Otherwise I am out of ideas - sorry. Good luck with dataset collections - there is still a lot of work that needs to be done in -central for collections for sure but I am really excited about the potential proteomics applications. -John cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Egg distribution error
Sorry for the delayed response - I am not really an expert on Galaxy's
egg stuff - but I believe running `python scripts/fetch_eggs.py`
before starting Galaxy usually fixes these problems for reasons I
don't understand. One probably shouldn't need to manually install mock
or pycrypto though.
Sorry for the problems and thanks for using Galaxy (and upgrading)!
-John
On Thu, Jan 15, 2015 at 10:42 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Hi all
For what it's worth, I manually installed mock (and pycrypto because
that was the next thing it complained about) and it worked after that.
Ulf
On 14/01/15 14:23, Ulf Schaefer wrote:
Hi all
After the announcements this morning, I upgraded to the latest stable
release as suggested (latest_2015.01.13).
Our server is now not starting with the following error message. Any
ideas what I might be doing wrong?
Thanks a lot
Ulf
---
galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg
galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in
the egg distribution.
galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency bioblend requires
mock
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
375, in loadobj
return context.create()
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
813, in create
return self.object_type.invoke(self)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
97, in fix_call
val = callable(*args, **kw)
File
/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line
54, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py,
line 119, in add_ui_controllers
module = import_module( module_name )
File
/home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 21, in module
eggs.require('bioblend')
File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
411, in require
return c[req.project_name].require()
File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
239, in require
dists = self.resolve()
File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
170, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File /home/galaxy/galaxy-dist/lib/pkg_resources.py, line 569, in
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg),
Requirement.parse('mock'))
---
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Re: [galaxy-dev] Egg distribution error
Hi all
For what it's worth, I manually installed mock (and pycrypto because
that was the next thing it complained about) and it worked after that.
Ulf
On 14/01/15 14:23, Ulf Schaefer wrote:
Hi all
After the announcements this morning, I upgraded to the latest stable
release as suggested (latest_2015.01.13).
Our server is now not starting with the following error message. Any
ideas what I might be doing wrong?
Thanks a lot
Ulf
---
galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg
galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in
the egg distribution.
galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency bioblend requires
mock
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
375, in loadobj
return context.create()
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
813, in create
return self.object_type.invoke(self)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
97, in fix_call
val = callable(*args, **kw)
File
/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line
54, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py,
line 119, in add_ui_controllers
module = import_module( module_name )
File
/home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 21, in module
eggs.require('bioblend')
File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
411, in require
return c[req.project_name].require()
File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
239, in require
dists = self.resolve()
File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
170, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File /home/galaxy/galaxy-dist/lib/pkg_resources.py, line 569, in
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg),
Requirement.parse('mock'))
---
**
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
**
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https://lists.galaxyproject.org/
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
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not be disclosed to any other person without the express
[galaxy-dev] Data manager for liftOver
Dear All, Could someone let me know if there is already a data manager tool for getting liftOver reference data within Galaxy or should I write one? Please let me know. Kind regards, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cruk.cam.ac.uk | +44 (0)1223 769 631 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
