Re: [galaxy-dev] Manually adding new tools from toolshed
I can try a local toolshed, but the organization I work at frowns upon automatic installation for various reasons. That and it lets me see exactly how a tool is installed and works within my local instance. When a tool is installed from the toolshed, how does Galaxy know about it? From a DB entry, or from the XML file(s) being present somewhere? I sort of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a user logs into a linux machine. This way, there is no modification of files, just placing the right files in the right directory is all that is needed. Anyway, I need to understand how Galaxy works with the toolshed. On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Ryan, what about a local bootstrapped ToolShed which is in sync with the public one (at least for the users you are interested on). Than you can install from this ToolShed. I guess this is less annoying than maintaining everything on your own. Cheers, Bjoern Am 16.01.2015 um 08:22 schrieb Peter Cock: On Thu, Jan 15, 2015 at 6:57 PM, Ryan G ngsbioinformat...@gmail.com wrote: 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 The old pre-ToolShed way to add a new datatype was indeed to add it to datatypes_conf.xml and put any Python file into the galaxy-dist/lib/galaxy/datatypes/ I'm still doing this on some of my locally developed tools, but now they are in the ToolShed perhaps I should switch to using that... Regards, Peter P.S. You also used to need to add an import line to the galaxy-dist/lib/galaxy/datatypes/registry.py but that is not longer required as of this bug fix: https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 ___ 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/
[galaxy-dev] Baltimore Area Galaxy Meetup @ Johns Hopkins, January 22
Hey Everyone! The Galaxy Project is holding a meetup style event https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22 on Thursday, January 22, starting at 6pm in the Department of Biology on the Homewood Campus. The meetup is open to anyone interested in analyzing the large datasets that are typical of contemporary research. Johns Hopkins is one of the two hubs for the project. We will be kicking things off with a discussion of Galaxy and how researchers around the world are leveraging it. See the meetup page https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22 for more information. Please RSVP http://bit.ly/1Bz3Nrk as space is limited. We are hoping this will be the first of many meetups, both in the Baltimore area, and elsewhere. If you are interested in hosting a meetup in your area, please contact Galaxy Outreach and we will help you get the word out. Thanks, Enis Afgan and Nitesh Turaga, of the Galaxy Team -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Unable to connect galaxy server after upgrade to latest version
I installed the latest galaxy server and started it without any change. The server stared on port 8080 and the log file looks fine. But when I typed http://localhost:8080, I got the error Unable to connect. I had worked with version 2014_08_11 and had no problem at all. What could have been wrong? ___ 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] new user : galaxy install error
**Did the following**
hg clone https://bitbucket.org/galaxy/galaxy-dist/ test
cd test/
hg update stable
Machine:
Mac Yosemite(10.10.1)
**Got the following error**
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 46, in module
c.resolve() # Only fetch eggs required by the config
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 347, in resolve
egg.resolve()
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 192, in resolve
if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range
Fetch failed.
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File /Users/apratap/softwares/test/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/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf, **context.local_conf)
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File /Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/buildapp.py,
line 54, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File /Users/apratap/softwares/test/lib/galaxy/web/framework/webapp.py,
line 119, in add_ui_controllers
module = import_module( module_name )
File
/Users/apratap/softwares/test/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 21, in module
eggs.require('bioblend')
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 411, in require
return c[req.project_name].require()
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 239, in require
dists = self.resolve()
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 170, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File /Users/apratap/softwares/test/lib/pkg_resources.py, line 569,
in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/Users/apratap/softwares/test/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('poster'))
galaxy.jobs.handler INFO 2015-01-16 16:40:58,095 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,096 job handler queue stopped
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to monitor thread
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to 3 worker threads
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LocalRunner: Sending
stop signal to 5 worker threads
galaxy.jobs.handler INFO 2015-01-16 16:40:58,097 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,098 job handler stop queue stopped
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Re: [galaxy-dev] new user : galaxy install error
It probably happens due to a system installed package conflict.
You should probably do it inside a virtual environment:
virtualenv --no-site-packages venv
source venv/bin/activate
cd galaxy-dist
sh run.sh
That should hopefully solve the problem.
On 16 January 2015 at 16:42, Abhishek Pratap abhishek@gmail.com wrote:
**Did the following**
hg clone https://bitbucket.org/galaxy/galaxy-dist/ test
cd test/
hg update stable
Machine:
Mac Yosemite(10.10.1)
**Got the following error**
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 46, in module
c.resolve() # Only fetch eggs required by the config
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 347, in resolve
egg.resolve()
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 192, in resolve
if e.args[1].key != e.args[0].key:
IndexError: tuple index out of range
Fetch failed.
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File /Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File /Users/apratap/softwares/test/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/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File
/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File
/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf, **context.local_conf)
File
/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File /Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/buildapp.py,
line 54, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File /Users/apratap/softwares/test/lib/galaxy/web/framework/webapp.py,
line 119, in add_ui_controllers
module = import_module( module_name )
File
/Users/apratap/softwares/test/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 21, in module
eggs.require('bioblend')
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 411, in require
return c[req.project_name].require()
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 239, in require
dists = self.resolve()
File /Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py,
line 170, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File /Users/apratap/softwares/test/lib/pkg_resources.py, line 569,
in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/Users/apratap/softwares/test/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('poster'))
galaxy.jobs.handler INFO 2015-01-16 16:40:58,095 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,096 job handler queue stopped
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to monitor thread
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending
stop signal to 3 worker threads
galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LocalRunner: Sending
stop signal to 5 worker threads
galaxy.jobs.handler INFO 2015-01-16 16:40:58,097 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2015-01-16 16:40:58,098 job handler stop queue
stopped
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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/
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