[galaxy-dev] errors after updating galaxy distribution
Hi, I updated my galaxy distribution with hg pull -u Then tried to re-run galaxy and got an error: $ ./run.sh Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 1049, in run invoke(command, command_name, options, args[1:]) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 1055, in invoke exit_code = runner.run(args) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 220, in run result = self.command() File /home/microbeco/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/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /home/microbeco/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /home/microbeco/galaxy-dist/lib/galaxy/web/buildapp.py, line 3, in module from galaxy.webapps.galaxy.buildapp import app_factory File /home/microbeco/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 16, in module import galaxy.model.mapping File /home/microbeco/galaxy-dist/lib/galaxy/model/mapping.py, line 14, in module from sqlalchemy.types import BigInteger ImportError: cannot import name BigInteger I also tried to update my database but got a different error: $ sh manage_db.sh upgrade 114 - 115... Traceback (most recent call last): File ./scripts/manage_db.py, line 62, in module main( repository=repo, url=db_url ) File /home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py, line 150, in main ret = command_func(**kwargs) File /home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py, line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File /home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py, line 349, in _migrate schema.runchange(ver, change, changeset.step) File /home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py, line 184, in runchange change.run(self.engine, step) File /home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py, line 101, in run func() TypeError: upgrade() takes exactly 1 argument (0 given) How can I fix this? Thanks, Dan ___ 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] routing to a cluster or not on a per-tool basis
On Tue, May 7, 2013 at 10:16 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Dan, Sure, you can configure per-tool job runners. This wiki page (http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started, but let me know if you run into any trouble. Thanks! Following up on this. As I mentioned before, this Galaxy instance was already configured to use the cluster by default. I did not set up the cluster or the Galaxy instance. This particular instance did not use the job_conf.xml file. But I updated it and set up a job_conf.xml and I was able to set it up so that some tools would be run on the local machine. However, in trying to get it set up so some jobs would run on the cluster (which is what happened by default before I came along) I ran into problems. Previously, it looked like the cluster stuff was configured in universe_wsgi.ini, and I guessed that these were the relevant lines: start_job_runners = drmaa default_cluster_job_runner = drmaa://-t 12:00 -A noaccount/ So I tried to move that setup to job_conf.xml: ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers handler id=main/ /handlers destinations default=local destination id=local runner=local/ destination id=cluster runner=drmaa param id=nativeSpecification-t 12:00 -A noaccount//param /destination /destinations tools !-- Tools can be configured to use specific destinations or handlers, identified by either the id or tags attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random. -- tool id=mytesttool destination=cluster/ /tools /job_conf When I run 'my test tool', however, it just hangs. Any tips? To answer my own question...I think I have gotten this working, by using the drmaa snippet from the job_conf.xml.sample_advanced file in my galaxy distro: destination id=real_user_cluster runner=drmaa !-- TODO: The real user options should maybe not be considered runner params. -- param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination If I set up my test tool to run with this destination, it works. Thanks, Dan Thanks, Dan On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi, I have some tools that run really quickly without using any kind of cluster. I would prefer not to run these tools on a cluster, as the overhead of submitting these jobs makes them take much longer than they otherwise would. I have other tools that are computationally intensive and need to be run on a cluster. I would like to expose all these tools in the same Galaxy instance, but have some tools run on the cluster and others not. Is this possible? Thanks, Dan ___ 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 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] routing to a cluster or not on a per-tool basis
On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Dan, Sure, you can configure per-tool job runners. This wiki page (http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started, but let me know if you run into any trouble. Thanks! Following up on this. As I mentioned before, this Galaxy instance was already configured to use the cluster by default. I did not set up the cluster or the Galaxy instance. This particular instance did not use the job_conf.xml file. But I updated it and set up a job_conf.xml and I was able to set it up so that some tools would be run on the local machine. However, in trying to get it set up so some jobs would run on the cluster (which is what happened by default before I came along) I ran into problems. Previously, it looked like the cluster stuff was configured in universe_wsgi.ini, and I guessed that these were the relevant lines: start_job_runners = drmaa default_cluster_job_runner = drmaa://-t 12:00 -A noaccount/ So I tried to move that setup to job_conf.xml: ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/ /plugins handlers handler id=main/ /handlers destinations default=local destination id=local runner=local/ destination id=cluster runner=drmaa param id=nativeSpecification-t 12:00 -A noaccount//param /destination /destinations tools !-- Tools can be configured to use specific destinations or handlers, identified by either the id or tags attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random. -- tool id=mytesttool destination=cluster/ /tools /job_conf When I run 'my test tool', however, it just hangs. Any tips? Thanks, Dan On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi, I have some tools that run really quickly without using any kind of cluster. I would prefer not to run these tools on a cluster, as the overhead of submitting these jobs makes them take much longer than they otherwise would. I have other tools that are computationally intensive and need to be run on a cluster. I would like to expose all these tools in the same Galaxy instance, but have some tools run on the cluster and others not. Is this possible? Thanks, Dan ___ 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 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] routing to a cluster or not on a per-tool basis
Hi, I have some tools that run really quickly without using any kind of cluster. I would prefer not to run these tools on a cluster, as the overhead of submitting these jobs makes them take much longer than they otherwise would. I have other tools that are computationally intensive and need to be run on a cluster. I would like to expose all these tools in the same Galaxy instance, but have some tools run on the cluster and others not. Is this possible? Thanks, Dan ___ 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] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto carlos.borr...@gmail.com wrote: On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Re: login: I believe there's a redirect in place that moves you past the older 'Return to the homepage' message automatically - I think you're good there (and logged in). Are you seeing the 'Logged in as your email' in the 'User' menu at the top? No. I think I'm not actually being logged in. All I see under the User menu is Login and Register. I realize this is a long thread and my recommendation might not help much or was done it already. Sorry if that's the case. This behavior is something I have seen often with Chrome in particular and 99% of the time is related to an old cookie. Specially when I'm accessing a different galaxy instance from the same URL I accessed a previous one, something I see Dan did at the beginning of this thread. I recommend erasing any cookie related to galaxy and also trying with a different browser. Firefox seems to work particularly fine. Indeed, it works with Firefox. And it works with Chrome after I delete my cookies. Thanks very much! Dan Hope it helps, Carlos ___ 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/
Re: [galaxy-dev] File Upload doesn't generate any activity
On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold sgroenew...@idtdna.com wrote: We’ve installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It’s as if the Execute button is disabled. I’ve tried changing the ajax-upload parameter to “false” in tools/data_source/upload.xml (as mentioned in a workaround posted to the list by Daniel Blankenburg in Aug 2012). I’ve also tried using different browsers (including Internet Explorer) and going the route of Adding Data Libraries as Admin. None of those attempts have worked. Am I missing a configuration setup? Could there be permissions issues on the Galaxy machine? This sounds like the same issue I've reported to this list, which Carl and others have been kind enough to look at. I think their look is still in progress but hopefully there will be some news about it soon. Here is that thread: http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installation-this-request-returned-None-from-get-history-td4657958.html#a4657960 Dan Thanks. Steve ___ 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/ ___ 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/
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Dan, Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the tip or a specific revision? I installed galaxy as recommended in the docs: hg clone https://bitbucket.org/galaxy/galaxy-dist/ When you see the Syntax error, does Galaxy continue to start up after and the upload error (AttributeError: 'NoneType' object has no attribute 'add') happens later? OK, now bizarrely I am having a slightly different problem, but AFAIK nothing has changed. I don't get that stack trace on startup and now I can upload pasted text, but I can't seem to upload files. I tried to upload a 3KB csv file called sample.csv and it shows up in history with the animated up arrow but the upload never finishes, and every 4 seconds the log shows: 127.0.0.1 - - [30/Jan/2013:11:10:09 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 No error message in the log though. So I can at least get past my initial place where I was stuck, because the tools I am developing need only text files as input (which can be pasted). I'd still like to know why I can't upload files (from the Choose File button on the Upload File page). Thanks for your help, Dan To make sure I'm understanding you correctly, you can find this error in the logs of both of your installations? Thanks, C On Tue, Jan 29, 2013 at 1:55 PM, Carl Eberhard carlfeberh...@gmail.com wrote: galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py, line 447, in _load_plugin module = __import__( module_name ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 232 worker = threading.Thread( ( name=LwrJobRunner.thread-%d % i ), target=self.run_next ) ^ SyntaxError: invalid syntax It is significant - and not normal behavior. Good catch! (You can disregard the 'Error: this request returned None from get_history()' message; it records the lack of a current history which is normal when you access those pages but haven't logged in yet) On Tue, Jan 29, 2013 at 12:49 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi Carl, On Tue, Jan 29, 2013 at 9:30 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Those are both fine then. You've got us (temporarily) stumped - even the old timers here. Can you give some rough information on your system - what OS you're using, what your network set up would be? Thanks again for looking into this. It's Mac OS X 10.8.2 with Chrome 24.0.1312.56, though I have the same problems with Safari 6.0.2 (8536.26.17) and Firefox 17.0. Python 2.7.2. Also - if it's not too problematic - can you do a fresh clone of Galaxy onto your system and see if that installation has the same problem? I did this and it seems to have pretty much the same problem but a slightly different manifestation. Now I am now getting the error message Error: this request returned None from get_history(): http://localhost:8080/; when I try and upload a file; instead, no error messages show up in the console, but the upload still fails. I do however get that error message when I try and log in as a user after registering that user. Another thing I notice, in the output immediately after starting run.sh: galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py, line 447, in _load_plugin module = __import__( module_name ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 232 worker = threading.Thread( ( name=LwrJobRunner.thread-%d % i ), target=self.run_next ) ^ SyntaxError: invalid syntax Maybe that is significant? Switching back to my previous distribution I get the identical behavior... Thanks, Dan C On Mon, Jan 28, 2013 at 5:03 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard carlfeberh...@gmail.com wrote: If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy? SQLAlchemy-0.5.6_dev_r6498-py2.7.egg Do you have SQLAlchemy installed already on that machine (apart from the one in Galaxy's eggs)? I don't think so. I never knowingly installed
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Wed, Jan 30, 2013 at 11:36 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Well - as long as those errors don't happen again - it may well be progress. For the next step, can you: 1. open Galaxy in Chrome 2. Go to the settings menu (the button with three horizontal bars on the right side of the address bar). 3. Click the Tools submenu 4. Click the Javascript Console option 5. Try to upload your csv file again This will see if there are any client side errors that are happening during the upload process. It shouldn't take to long to see them if they're there. Nothing shows up in the javascript console. You may also want to post some of the server log information. Specifically, (around the time you start the failing upload) any lines you see that start with galaxy.jobs (e.g. galaxy.jobs.manager, galaxy.jobs.runners, etc.). I don't see any such lines, just this: 127.0.0.1 - - [30/Jan/2013:11:46:21 -0700] POST /tool_runner/upload_async_create HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:21 -0700] GET /tool_runner/upload_async_message HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:21 -0700] GET /history HTTP/1.1 200 - http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:21 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:25 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:29 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:33 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [30/Jan/2013:11:46:38 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 And the last line repeats every 4 seconds (with timestamp updated). Dan C On Wed, Jan 30, 2013 at 2:13 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Dan, Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the tip or a specific revision? I installed galaxy as recommended in the docs: hg clone https://bitbucket.org/galaxy/galaxy-dist/ When you see the Syntax error, does Galaxy continue to start up after and the upload error (AttributeError: 'NoneType' object has no attribute 'add') happens later? OK, now bizarrely I am having a slightly different problem, but AFAIK nothing has changed. I don't get that stack trace on startup and now I can upload pasted text, but I can't seem to upload files. I tried to upload a 3KB csv file called sample.csv and it shows up in history with the animated up arrow but the upload never finishes, and every 4 seconds the log shows: 127.0.0.1 - - [30/Jan/2013:11:10:09 -0700] GET /api/histories/8237ee2988567c1c HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 No error message in the log though. So I can at least get past my initial place where I was stuck, because the tools I am developing need only text files as input (which can be pasted). I'd still like to know why I can't upload files (from the Choose File button on the Upload File page). Thanks for your help, Dan To make sure I'm understanding you correctly, you can find this error in the logs of both of your installations? Thanks, C On Tue, Jan 29, 2013 at 1:55 PM, Carl Eberhard carlfeberh...@gmail.com wrote: galaxy.jobs.handler DEBUG 2013-01-29 09:43:52,107 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.handler ERROR 2013-01-29 09:43:52,111 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@gmail.com wrote:
I was incorrect in stating that the changes in the next galaxy-dist will
help in this case, unfortunately. From the stack trace you posted, there is
a deeper error with your instance that the client-side changes won't help.
Can you post the size, type, and name of the file you're trying to upload?
I can reproduce this by just typing hello, world into the
URL/Text: box on the Upload File page. Any file of any type seems
to trigger this problem.
Thanks,
Dan
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Another thing you might try is to upload the file to our test server:
https://test.g2.bx.psu.edu/ and see if that works.
Thanks, that does work.
Setting up an FTP server on my local installation seems pretty
complex. All I really want to do is work around this issue and fool
Galaxy into thinking that I have uploaded a file using the
uploader...since this is a local installation I can put a file
anywhere on my system, I don't have to actually upload it, just place
it in a directory.
If there is no such workaround, I'll wait for the fix, I guess. Thanks
very much for working on this!
Dan
On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
If this is happening consistently and a refresh on the history isn't
doing
anything, you might try ftp upload:
http://wiki.galaxyproject.org/FTPUpload
or if you have permissions or are an admin you can try uploading to a
data
library:
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
What sort of database are you using on your local instance?
The default (sqlite I guess). It's a completely vanilla instance, I
have not touched the config files.
Dan
On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Thanks, Dan. That helps and I'll start looking into this.
We will be pushing out a new galaxy-dist revision sometime this
week
if
all
goes well. This revision includes some code for the history panel
that
may
help handle this situation a bit better. I'd recommend updating
to
that
revision when it comes out.
Thanks! Is there a workaround to upload a file or add it to my
history
in the meantime? Command-line is ok. If there isn't one, that's ok
too
Dan
I'll let you know what I can find.
Carl
On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Heya, Dan.
Sorry for the trouble.
When you get that error again look for a line like you have
above:
Debug at: http://localhost:8080/_debug/view/1358978130
If you open a new tab or window in your browser and go to the
address
('http://localhost:8080/_debug ...'), you should see a more
informative
error message - complete with a list of function calls that
led
to
the
error
(a stack trace).
Can you post that stack trace when you see it?
Thanks for the quick response. Here it is:
URL: http://localhost:8080/tool_runner/upload_async_create
File
'/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File
'/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File
'/Users/dtenenba/dev/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 73 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs
Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard carlfeberh...@gmail.com wrote:
If you go to your galaxy root in a terminal and then cd to eggs, what is the
version listed for SQLAlchemy?
SQLAlchemy-0.5.6_dev_r6498-py2.7.egg
Do you have SQLAlchemy installed already on that machine (apart from the one
in Galaxy's eggs)?
I don't think so. I never knowingly installed it and in a fresh python
session, 'import sqlalchemy' returns an error that there is no such
module.
Thanks,
Dan
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
I was incorrect in stating that the changes in the next galaxy-dist will
help in this case, unfortunately. From the stack trace you posted, there
is
a deeper error with your instance that the client-side changes won't
help.
Can you post the size, type, and name of the file you're trying to
upload?
I can reproduce this by just typing hello, world into the
URL/Text: box on the Upload File page. Any file of any type seems
to trigger this problem.
Thanks,
Dan
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Another thing you might try is to upload the file to our test server:
https://test.g2.bx.psu.edu/ and see if that works.
Thanks, that does work.
Setting up an FTP server on my local installation seems pretty
complex. All I really want to do is work around this issue and fool
Galaxy into thinking that I have uploaded a file using the
uploader...since this is a local installation I can put a file
anywhere on my system, I don't have to actually upload it, just place
it in a directory.
If there is no such workaround, I'll wait for the fix, I guess. Thanks
very much for working on this!
Dan
On Wed, Jan 23, 2013 at 6:06 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
If this is happening consistently and a refresh on the history isn't
doing
anything, you might try ftp upload:
http://wiki.galaxyproject.org/FTPUpload
or if you have permissions or are an admin you can try uploading to
a
data
library:
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
On Wed, Jan 23, 2013 at 5:44 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:42 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
What sort of database are you using on your local instance?
The default (sqlite I guess). It's a completely vanilla instance, I
have not touched the config files.
Dan
On Wed, Jan 23, 2013 at 5:37 PM, Dan Tenenbaum
dtene...@fhcrc.org
wrote:
On Wed, Jan 23, 2013 at 2:35 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Thanks, Dan. That helps and I'll start looking into this.
We will be pushing out a new galaxy-dist revision sometime
this
week
if
all
goes well. This revision includes some code for the history
panel
that
may
help handle this situation a bit better. I'd recommend
updating
to
that
revision when it comes out.
Thanks! Is there a workaround to upload a file or add it to my
history
in the meantime? Command-line is ok. If there isn't one, that's
ok
too
Dan
I'll let you know what I can find.
Carl
On Wed, Jan 23, 2013 at 5:18 PM, Dan Tenenbaum
dtene...@fhcrc.org
wrote:
Hi Carl,
On Wed, Jan 23, 2013 at 2:14 PM, Carl Eberhard
carlfeberh...@gmail.com
wrote:
Heya, Dan.
Sorry for the trouble.
When you get that error again look for a line like you have
above:
Debug at: http://localhost:8080/_debug/view/1358978130
If you open a new tab or window in your browser and go to
the
address
('http://localhost:8080/_debug ...'), you should see a more
informative
error message - complete with a list of function calls that
led
to
the
error
(a stack trace).
Can you post that stack trace when you see it?
Thanks for the quick response. Here it is:
URL: http://localhost:8080/tool_runner/upload_async_create
File
'/Users/dtenenba/dev/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/Users/dtenenba/dev/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
[galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()
Hi, I installed galaxy completely from scratch: rm -rf galaxy-dist hg clone https://bitbucket.org/galaxy/galaxy-dist/ I'm not a mercurial expert but I think I have changeset 8530:a4113cc1cb5e; at least that's the first entry in hg log. Then started galaxy like this: cd galaxy-dist ./run.sh I went to http://localhost:8080 and tried to upload a file. I never saw the file in my history, and this is what printed out in the console after I clicked Execute on the Upload File page: galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,573 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-01-23 13:56:11,574 Error: this request returned None from get_history(): http://localhost:8080/tool_runner/upload_async_create 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] POST /tool_runner/upload_async_create HTTP/1.1 500 - http://localhost:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 Debug at: http://localhost:8080/_debug/view/1358978130 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] GET /tool_runner/upload_async_message HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 127.0.0.1 - - [23/Jan/2013:13:56:11 -0700] GET /history HTTP/1.1 200 - http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 Hope someone can help. Thanks, Dan ___ 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/
Re: [galaxy-dev] filtering a param of type 'data' so only one type is available
On Wed, Jan 23, 2013 at 3:51 PM, Ross ross.laza...@gmail.com wrote: Hi, Dan. Using format=rda will restrict the list to history items of the 'rda' datatype - but ONLY if the rda datatype has been defined! The easiest way to do that is to define a new datatype in datatypes_conf.xml and since rData is binary, you should subclass binary. Something like (untested - especially the mimetype !) datatype extension=rda type=galaxy.datatypes.binary:Binary mimetype=application/x-rlang-transport subclass=True / might work. A server restart is always required to load any new datatypes. Good luck! It works! I changed the mime type to application/x-gzip, since serialized R objects are gzipped. Thanks, Dan On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi, I have a tool wrapper with a param of type=data. Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format=rda and that didn't seem to change anything. 2) rda is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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/
Re: [galaxy-dev] filtering a param of type 'data' so only one type is available
On Wed, Jan 23, 2013 at 4:03 PM, Ross ross.laza...@gmail.com wrote: Hi, Dan Glad it worked and thanks for pointing out a more general mimetype - does any one else (other than me) want to vote to add datatype extension=rda type=galaxy.datatypes.binary:Binary mimetype=application/x-gzip subclass=True / to datatypes_conf.xml.sample permanently ? I do. This would be great as I am automating the creation of galaxy tools and I'd like to be able to enable this feature without requiring (either manual or programmatic) editing of datatypes_conf.xml. Note that serialized R objects also sometimes have the .RData extension -- both are valid -- so it would be good to support that as well. But now that I think about it, serialized objects are not always gzip files--depending on the value of the 'compression' flag used with the save() function, it may be gzip, bzip, xz, or even ascii! So maybe the mime type should be changed back to something different, like application/x-rlang-transport as you suggested. I tried this and it seemed to work; It did the filtering I wanted and I was still able to download a history item with this type. Dan Thanks, Dan On Thu, Jan 24, 2013 at 10:58 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Wed, Jan 23, 2013 at 3:51 PM, Ross ross.laza...@gmail.com wrote: Hi, Dan. Using format=rda will restrict the list to history items of the 'rda' datatype - but ONLY if the rda datatype has been defined! The easiest way to do that is to define a new datatype in datatypes_conf.xml and since rData is binary, you should subclass binary. Something like (untested - especially the mimetype !) datatype extension=rda type=galaxy.datatypes.binary:Binary mimetype=application/x-rlang-transport subclass=True / might work. A server restart is always required to load any new datatypes. Good luck! It works! I changed the mime type to application/x-gzip, since serialized R objects are gzipped. Thanks, Dan On Thu, Jan 24, 2013 at 10:41 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi, I have a tool wrapper with a param of type=data. Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format=rda and that didn't seem to change anything. 2) rda is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan ___ 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/ ___ 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/
[galaxy-dev] Error trying to run functional tests on a single tool
Hi, I'm trying to test out the functional testing mechanism by running it on an existing Galaxy tool. First I ran ./run_functional_tests.sh -list which produced a list of tools I can test. I chose 'vcf_annotate' and tested it as follows: ./run_functional_tests.sh -id vcf_annotate This produced a lot of output which included an exception trace. The output was not conclusive as to whether the test ran or was successful. The output is too long for this mailing list but you can find it here: https://gist.github.com/3988398 I am reluctant to try and excerpt the relevant bits because it's hard for me to know what is relevant and what is not. I am running the latest Galaxy (just did hg pull/hg update and migrated). This is on a Mac OS X 10.7.4 machine with python 2.7. When I run the same command on a linux machine, it works (though it took me a while to find the test output; it was buried in a lot of output that also contained (apparently irrelevant) stack traces). So perhaps there is something wrong with my configuration. Hope someone can help me out. Also had a couple of newbie questions about the functional test framework. 1) Why does it use tool_conf.xml.sample instead of tool_conf.xml? Can I change it to use tool_conf.xml? This way I do not need to add tools to two places in order to test them. (Plus the name of tool_conf.xml.sample indicates that it is just a demo file). 2) run_functional_tests.sh -list lists tools (such as 'upload1') that do not have functional tests, so cannot (if my understanding is correct) be tested with this script. Perhaps it would make more sense not to list these tools? Thanks, Dan ___ 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/
[galaxy-dev] Error when param has no value and type is float or integer
Hi, If I have a tool wrapper with this: param name=x type=integer help=the x param/ I get an error when I start Galaxy: galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from path: RGalaxy_test_tool/foo.xml Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 332, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 450, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 788, in __init__ self.parse( root, guid=guid ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 959, in parse self.parse_inputs( root ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 1043, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 1439, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 1532, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py, line 1544, in parse_param_elem param = ToolParameter.build( self, input_elem ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 176, in build return parameter_types[param_type]( tool, param ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 228, in __init__ raise ValueError( The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer % self.name ) ValueError: The settings for the field named 'x' require a 'value' setting and optionally a default value which must be an integer However, according to the documentation: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set The value attribute to the param tag is not required. It's easy to work around this, by adding value=, but I'm wondering if it's a bug, documentation or otherwise. Thanks, Dan ___ 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/
[galaxy-dev] creating a galaxy dataset within a galaxy tool
I'd like to have a tool that does not actually return anything (is that possible?) but writes a file to the directory where Galaxy stores uploaded data files, and tells Galaxy about it (perhaps that involves writing to a database?). My tool is written in R. Here is my scenario: I want the user to upload a text file, then pass that text file, along with several parameters, (in something we'll call Tool1) which I use to create a serialized R object. That object is then used in several other tools. I don't want the user to have to download and then re-upload the serialized object. I want it to just be available after the user runs Tool1. I realize that workflows could solve my problem here, but I want to keep the UI as simple as possible. For Tool2..ToolN, I don't want to have to always ask the user for the parameters for Tool1 as well as the current tool. So, is there a way for my tool to make Galaxy aware of an additional dataset? Thanks Dan ___ 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/
Re: [galaxy-dev] creating a galaxy dataset within a galaxy tool
Hi James, I realize I didn't do a good job explaining, but your suggestion sounds promising. How can I make something into a dataset? Here's what I'm hoping to achieve: User runs Tool1, uploading a text file and specifying some parameters. Tool1 uses this to write out a serialized R object. Somehow this object is persisted in Galaxy (made into a dataset). Now the user can run Tool2 or Tool3, which each take the dataset created in the previous step, plus some parameters of their own. So I guess the only part I am missing is how to turn the output of Tool1 into a dataset. Is there a way to do this other than downloading it to my local computer and then uploading it to Galaxy? That seems awkward Thanks, Dan On Tue, Sep 18, 2012 at 3:41 PM, James Taylor ja...@jamestaylor.org wrote: Dan, I may not be following, but why not make the serialized R object a dataset (of its own datatype). Then the user can just pass it to the downstream tools just by specifying one parameter. -- jt On Tue, Sep 18, 2012 at 3:00 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: I want the user to upload a text file, then pass that text file, along with several parameters, (in something we'll call Tool1) which I use to create a serialized R object. That object is then used in several other tools. I don't want the user to have to download and then re-upload the serialized object. I want it to just be available after the user runs Tool1. ___ 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/
[galaxy-dev] select with =20 options renders as autocompleting text box
Hi, I notice that a param with type select renders differently depending on how many options there are. If there are 20 options, it appears as a normal select box. If there are = 20 options, it looks like a text box (but it has autocompletion and does have a dropdown menu), and Inspect Element in Chrome reveals that it in fact is an input type=text with the classes text-and-autocomplete-select ac_input. Is this deliberate? If so, can the behavior be turned off? I suppose that there is no functional impact, but it looks sort of odd and jarring to have several select boxes one of which happens to look different just because of the number of options it has. Example: param name=distance type=select help= label=Distance Method force_select=FALSE option value=None1/option /param ...renders as a normal select box. param name=distance type=select help= label=Distance Method force_select=FALSE option value=None1/option option value=None2/option option value=None3/option option value=None4/option option value=None5/option option value=None6/option option value=None7/option option value=None8/option option value=None9/option option value=None10/option option value=None11/option option value=None12/option option value=None13/option option value=None14/option option value=None15/option option value=None16/option option value=None17/option option value=None18/option option value=None19/option option value=None20/option /param ...renders as a text box with autocomplete. Thanks, Dan ___ 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/
Re: [galaxy-dev] using data_ref to refer to column names?
So, sounds like maybe this feature does not existI'd like to request it (given a dataset, I'd like to be able to show the column headers of that dataset in a select box). Thanks, Dan On Wed, Aug 29, 2012 at 11:09 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi, I have some code that makes a plot and creates a legend from a given column name in the user's input data, which may have arbitrary column names. I'd like to create a dropdown list that has all the column names in it, but I don't know the names beforehand; I won't know them until the user uploads their data file. So all I can do is have a freeform text box where I ask the user to type a column name, which seems error-prone and ugly. I notice that the XY plotting tool has something sort of like this, where it can tell how many columns are in your dataset and lets you choose them, but it calls the columns c1, c2, etc. My datasets have a header line with column names and I want to show the actual column name, not reference them by column number. Is this possible? Is there a solution to this? I have a number of use cases like this, so it would be great if there was. Thanks, Dan ___ 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/
Re: [galaxy-dev] using data_ref to refer to column names?
On Tue, Sep 4, 2012 at 4:57 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Sep 4, 2012 at 4:54 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: So, sounds like maybe this feature does not existI'd like to request it (given a dataset, I'd like to be able to show the column headers of that dataset in a select box). Thanks, Dan No, it doesn't, but I'd like it too: https://bitbucket.org/galaxy/galaxy-central/issue/554/show-column-names-headers-or-first-entry Thanks much. Strong +1 from me. Dan Peter ___ 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/
[galaxy-dev] using data_ref to refer to column names?
Hi, I have some code that makes a plot and creates a legend from a given column name in the user's input data, which may have arbitrary column names. I'd like to create a dropdown list that has all the column names in it, but I don't know the names beforehand; I won't know them until the user uploads their data file. So all I can do is have a freeform text box where I ask the user to type a column name, which seems error-prone and ugly. I notice that the XY plotting tool has something sort of like this, where it can tell how many columns are in your dataset and lets you choose them, but it calls the columns c1, c2, etc. My datasets have a header line with column names and I want to show the actual column name, not reference them by column number. Is this possible? Is there a solution to this? I have a number of use cases like this, so it would be great if there was. Thanks, Dan ___ 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/
[galaxy-dev] grouping/separating parameters on the page
Hello, Is there a way to do one or both of the following: 1) Group a set of related parameters together on a tool page 2) Put a separator in between related groups. I have a tool with lots of parameters. It's ok to have them all on one page but I'd like to have some space or a line between the related groups (and maybe even a header for the group) so that users know which parameters are related. Thanks, Dan ___ 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/
Re: [galaxy-dev] Conditionally showing certain form elements on tool page
Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/ Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: inputs param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param param name=param2 type=select label=filter2Name help=more helpful tips option value=yesyes/option option value=nono/option /param /inputs I had certain options that WERE mutually exclusive, and required nested conditional statements, where I had an outer conditional for the extra options, and an inner conditional around each parameter. As for the command tag, the select type parameters make it easy because you can just check the string values with an if statement, like so: (assuming python) command interpreter=python tool.py #if $param1 == yes: --YourGetOptFlag #else: ##dont even need an else, just ignore #end if /command If I am not mistaken, this should be sufficient if all you need to pass is a flag indicating your program to use the filter. If you need to pass a flag AND integer values, you are going to have to wrap your parameters in conditional tags and use a set of when: inputs conditional name=firstConditional param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param when value=yes param name=IntegerBox type=integer value=[default value] min=(optional) max=(optional) label=UseParamName help=helpful text / /when when value=no / !--Doesnt show integer text box when no is chosen in the select-- /conditional /inputs Rinse and repeat, adding conditionals around each select. I think this is actually what you want to do, as you say you want a box to appear after a user selects whether or not to use the filter. Also, quick note, the text between the option tags are what appear on the select buttons, so they can be whatever you want. The value= is the important thing, as this is what you will evaluate the if/else to in the command tag. One last thing, The cheetah command is really no different. command interpreter=python tool.py #if $firstConditional.param1 == yes: --testGetOpt $firstConditional.IntegerBox #end if /command The second command tag is how I pass a few parameters into my command line tool. Anyway, I hope this helped a little bit. If you need anything else, let me know and I will see If I can help
Re: [galaxy-dev] Conditionally showing certain form elements on tool page
On Thu, Aug 16, 2012 at 10:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/ Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: inputs param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param param name=param2 type=select label=filter2Name help=more helpful tips option value=yesyes/option option value=nono/option /param /inputs I had certain options that WERE mutually exclusive, and required nested conditional statements, where I had an outer conditional for the extra options, and an inner conditional around each parameter. As for the command tag, the select type parameters make it easy because you can just check the string values with an if statement, like so: (assuming python) command interpreter=python tool.py #if $param1 == yes: --YourGetOptFlag #else: ##dont even need an else, just ignore #end if /command If I am not mistaken, this should be sufficient if all you need to pass is a flag indicating your program to use the filter. If you need to pass a flag AND integer values, you are going to have to wrap your parameters in conditional tags and use a set of when: inputs conditional name=firstConditional param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param when value=yes param name=IntegerBox type=integer value=[default value] min=(optional) max=(optional) label=UseParamName help=helpful text / /when when value=no / !--Doesnt show integer text box when no is chosen in the select-- /conditional /inputs Rinse and repeat, adding conditionals around each select. I think this is actually what you want to do, as you say you want a box to appear after a user selects whether or not to use the filter. Also, quick note, the text between the option tags are what appear on the select buttons, so they can be whatever you want. The value= is the important thing, as this is what you will evaluate the if/else to in the command tag. One last thing, The cheetah command is really no different. command interpreter=python tool.py #if $firstConditional.param1 == yes: --testGetOpt $firstConditional.IntegerBox #end if /command The second command tag is how I pass a few parameters into my command line tool. Anyway, I hope this helped a little
Re: [galaxy-dev] Conditionally showing certain form elements on tool page
Hi John and Peter, On Thu, Aug 16, 2012 at 11:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Aug 16, 2012 at 6:53 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: ... This is extremely helpful! Thanks. I find the select box yes/no idiom a bit awkward. I'd prefer a checkbox (just a single one, not one each for yes and no) but doing a select box is ok too, I can live with that. Using a boolean checkbox should work - although early on it wasn't possible thus many older tools use a select instead: https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional I can do a checkbox like this: param name=cbtest type=boolean label=checkbox help=some help/ But I want to have a checkbox that triggers some other params to appear when it is checked (the way I have successfully done it with a select). I haven't been able to figure that out. If I do this: conditional name=thirdConditional param name=param2 type=boolean value=yes label=Filter 3 help=helpful tips / when value=yes param name=IntegerBox3 type=integer value=1 min=0 max=5 label=A parameter to filter 3 help=helpful text / /when when value=no / /conditional ...nothing happens when I click the checkbox. I also tried using a select with multiple=true and display=checkbox, but Galaxy doesn't like that because I provide only one option (yes). If you could tell me how to cause params to appear/disappear by checking a checkbox that would be great! Thanks, Dan Peter ___ 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/
[galaxy-dev] Conditionally showing certain form elements on tool page
Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/
Re: [galaxy-dev] Creating a galaxy tool in R - You must not use 8-bit bytestrings
Hello Hans-Rudolph, On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Dan There seems to be several issues connected with each other or not, I don't know. - Let's start with the 'curiosity': Do you get this problem with any tool? No. And, I should be a bit more specific about what happens. When I click execute I see this: The following job has been successfully added to the queue: 36: RNASeq tool on data 3 and data 4 37: RNASeq tool on data 3 and data 4 Does it also happen with a 'simple' (ie not using R) tool you add? No. - When you execute your R script on the command line, are you running it as the same user as Galaxy executes the job? Yes. - we execute R scripts the following way: commandRscript --vanilla /full path to script/script.R -n $name -i $infile -o $outfile/command and in the R script we use the library 'getopt' Good idea. Taking a closer, look, I found my R script was not expecting arguments in the same order that the XML script provided them in. I fixed that and now the R script runs without warning or error, but I still get the 8-bit bytestrings error, and the error Unable to finish job. However, by printing out the arguments within R, I can see the name of the output files that are supposed to be generated, and it looks like they are generated. So why doesn't the job finish? I think the 8 bit bytestrings error might be because R outputs backticks (`) and they show up escaped in the galaxy error like this: \xe2\x80\x98. Is there some way that I can set my LOCALE so that R uses an encoding that galaxy is happier with? Or perhaps I can get R to stop outputting those backticks somehow. I hope this get's you a little bit further. Thanks much, Dan Regards, Hans On 04/24/2012 11:56 PM, Dan Tenenbaum wrote: Apologies for originally posting this to galaxy-user; now I realize it belongs here. Hello, I'm a galaxy newbie and running into several issues trying to adapt an R script to be a galaxy tool. I'm looking at the XY plotting tool for guidance (tools/plot/xy_plot.xml), but I decided not to embed my script in XML, but instead have it in a separate script file, that way I can still run it from the command line and make sure it works as I make incremental changes. (So my script starts with args- commandArgs(TRUE)). Also, if it doesn't work, this suggests to me that there is a problem with my galaxy configuration. First, I tried using the r_wrapper.sh script that comes with the XY plotting tool, but it threw away my arguments: An error occurred running this job: ARGUMENT '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_4.dat' __ignored__ ARGUMENT '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_3.dat' __ignored__ ARGUMENT 'Fly' __ignored__ ARGUMENT 'Tagwise' __ignored__ etc. So then I tried just switching to Rscript: command interpreter=bashRscript RNASeq.R $countsTsv $designTsv $organism $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2/command (My script produces as output a csv file and a pdf file. The final two arguments I'm passing are the names of those files.) But then I get an error that Rscript can't be found. So I wrote a little wrapper script, Rscript_wrapper.sh: #!/bin/sh Rscript $* And called that: command interpreter=bashRscript_wrapper.sh RNASeq.R $countsTsv $designTsv $organism $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2/command Then I got an error that RNASeq.R could not be found. So then I added the absolute path to my R script to thecommand tag. This seemed to work (that is, it got me further, to the next error), but I'm not sure why I had to do this; in all the other tools I'm looking at, the directory to the script to run does not have to be specified; I assumed that the command would run in the appropriate directory. So now I've specified the full path to my R script: command interpreter=bashRscript_wrapper.sh /Users/dtenenba/dev/galaxy-dist/tools/bioc/RNASeq.R $countsTsv $designTsv $organism $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2/command And I get the following long error, which includes all of the output of my R script: Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 133, in run_job job_wrapper.finish( stdout, stderr ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/__init__.py, line 725, in finish self.sa_session.flush() File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py, line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py, line 1356, in flush self._flush(objects) File
Re: [galaxy-dev] Creating a galaxy tool in R - You must not use 8-bit bytestrings
On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hello Hans-Rudolph, On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Dan There seems to be several issues connected with each other or not, I don't know. - Let's start with the 'curiosity': Do you get this problem with any tool? No. And, I should be a bit more specific about what happens. When I click execute I see this: The following job has been successfully added to the queue: 36: RNASeq tool on data 3 and data 4 37: RNASeq tool on data 3 and data 4 Does it also happen with a 'simple' (ie not using R) tool you add? No. - When you execute your R script on the command line, are you running it as the same user as Galaxy executes the job? Yes. - we execute R scripts the following way: commandRscript --vanilla /full path to script/script.R -n $name -i $infile -o $outfile/command and in the R script we use the library 'getopt' Good idea. Taking a closer, look, I found my R script was not expecting arguments in the same order that the XML script provided them in. I fixed that and now the R script runs without warning or error, but I still get the 8-bit bytestrings error, and the error Unable to finish job. However, by printing out the arguments within R, I can see the name of the output files that are supposed to be generated, and it looks like they are generated. So why doesn't the job finish? I think the 8 bit bytestrings error might be because R outputs backticks (`) and they show up escaped in the galaxy error like this: \xe2\x80\x98. Is there some way that I can set my LOCALE so that R uses an encoding that galaxy is happier with? Or perhaps I can get R to stop outputting those backticks somehow. Answering my own question here (but following up with more questions). R was ouputting not backticks but curly quotes, and I turned these off by putting: options(useFancyQuotes = FALSE) in my R script. However, my R script is still failing: Dataset generation errors Dataset 46: RNASeq tool on data 3 and data 4 Tool execution generated the following error message: BiocInstaller version 1.5.7, ?biocLite for help Loading required package: org.Dm.eg.db Loading required package: AnnotationDbi Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation(Biobase)', and for packages 'citation(pkgname)'. Loading required package: DBI Calculating library sizes from column totals. Running estimateCommonDisp() on DGEList object before proceeding with estimateTagwiseDisp(). The tool produced the following additional output: pdf_outfile= /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_46.dat csv_outfile= /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_47.dat pdf 2 The thing is, none of this is an error. This is the exact output the script is supposed to produce, and it prints out the filenames of the two output files it creates, and I can verify that those exist and have the correct contents. So why does it say there is an error? Could it be the return code? I added q(save=no, status=0) to the end of the R script to ensure that the script exits with status code 0, but that did not change the error I got. So I am not sure how to solve this. The script works exactly as it's supposed to and creates the desired output, but tells me there is an error, and gives no way through the web interface to retrive the created output file. Also, I found out why two jobs were started each time I click Execute. It's because I had two files in my outputs section: outputs data format=pdf name=out_file1 / data format=csv name=out_file2 / /outputs Because my script generates two output files, a csv and a PDF. I took out the first data line above, and stopped passing the corresponding argument to my script, and the script no longer creates the PDF. Now the job only runs once each time I click Execute. But I would like the script to once again produce both output files. So, perhaps it was doing the right thing all along...showing one dataset in the history panel for each output file produced. Looking through the galaxy distribution, I see at least one other tool that does the same thing. So, sorry for the noise on this. In any case, I still get the same error described above even when only one output file is produced. Thanks, Dan I hope this get's you
Re: [galaxy-dev] Creating a galaxy tool in R - You must not use 8-bit bytestrings
On Wed, Apr 25, 2012 at 11:48 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hello Hans-Rudolph, On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Dan There seems to be several issues connected with each other or not, I don't know. - Let's start with the 'curiosity': Do you get this problem with any tool? No. And, I should be a bit more specific about what happens. When I click execute I see this: The following job has been successfully added to the queue: 36: RNASeq tool on data 3 and data 4 37: RNASeq tool on data 3 and data 4 Does it also happen with a 'simple' (ie not using R) tool you add? No. - When you execute your R script on the command line, are you running it as the same user as Galaxy executes the job? Yes. - we execute R scripts the following way: commandRscript --vanilla /full path to script/script.R -n $name -i $infile -o $outfile/command and in the R script we use the library 'getopt' Good idea. Taking a closer, look, I found my R script was not expecting arguments in the same order that the XML script provided them in. I fixed that and now the R script runs without warning or error, but I still get the 8-bit bytestrings error, and the error Unable to finish job. However, by printing out the arguments within R, I can see the name of the output files that are supposed to be generated, and it looks like they are generated. So why doesn't the job finish? Sorry for the noise of answering my own question, which I find has been asked and answered before, but perhaps this will help someone. Here's the answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003161.html Basically, if any output goes to STDERR, galaxy considers that the job failed. The link above suggests to do this: jobcommand ARGS 2/dev/null But I changed that to: jobcommand ARGS 21 that way, STDERR is redirected to STDOUT and any important diagnostic information originally printed to STDERR is not lost. I added this to my Rscript_wrapper.sh script and all is well. Thanks, Dan I think the 8 bit bytestrings error might be because R outputs backticks (`) and they show up escaped in the galaxy error like this: \xe2\x80\x98. Is there some way that I can set my LOCALE so that R uses an encoding that galaxy is happier with? Or perhaps I can get R to stop outputting those backticks somehow. Answering my own question here (but following up with more questions). R was ouputting not backticks but curly quotes, and I turned these off by putting: options(useFancyQuotes = FALSE) in my R script. However, my R script is still failing: Dataset generation errors Dataset 46: RNASeq tool on data 3 and data 4 Tool execution generated the following error message: BiocInstaller version 1.5.7, ?biocLite for help Loading required package: org.Dm.eg.db Loading required package: AnnotationDbi Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation(Biobase)', and for packages 'citation(pkgname)'. Loading required package: DBI Calculating library sizes from column totals. Running estimateCommonDisp() on DGEList object before proceeding with estimateTagwiseDisp(). The tool produced the following additional output: pdf_outfile= /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_46.dat csv_outfile= /Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_47.dat pdf 2 The thing is, none of this is an error. This is the exact output the script is supposed to produce, and it prints out the filenames of the two output files it creates, and I can verify that those exist and have the correct contents. So why does it say there is an error? Could it be the return code? I added q(save=no, status=0) to the end of the R script to ensure that the script exits with status code 0, but that did not change the error I got. So I am not sure how to solve this. The script works exactly as it's supposed to and creates the desired output, but tells me there is an error, and gives no way through the web interface to retrive the created output file. Also, I found out why two jobs were started each time I click Execute. It's because I had two files in my outputs section: outputs data format=pdf name=out_file1 / data format=csv name=out_file2
[galaxy-dev] Creating a galaxy tool in R - You must not use 8-bit bytestrings
Apologies for originally posting this to galaxy-user; now I realize it belongs here. Hello, I'm a galaxy newbie and running into several issues trying to adapt an R script to be a galaxy tool. I'm looking at the XY plotting tool for guidance (tools/plot/xy_plot.xml), but I decided not to embed my script in XML, but instead have it in a separate script file, that way I can still run it from the command line and make sure it works as I make incremental changes. (So my script starts with args - commandArgs(TRUE)). Also, if it doesn't work, this suggests to me that there is a problem with my galaxy configuration. First, I tried using the r_wrapper.sh script that comes with the XY plotting tool, but it threw away my arguments: An error occurred running this job: ARGUMENT '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_4.dat' __ignored__ ARGUMENT '/Users/dtenenba/dev/galaxy-dist/database/files/000/dataset_3.dat' __ignored__ ARGUMENT 'Fly' __ignored__ ARGUMENT 'Tagwise' __ignored__ etc. So then I tried just switching to Rscript: command interpreter=bashRscript RNASeq.R $countsTsv $designTsv $organism $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2/command (My script produces as output a csv file and a pdf file. The final two arguments I'm passing are the names of those files.) But then I get an error that Rscript can't be found. So I wrote a little wrapper script, Rscript_wrapper.sh: #!/bin/sh Rscript $* And called that: command interpreter=bashRscript_wrapper.sh RNASeq.R $countsTsv $designTsv $organism $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2/command Then I got an error that RNASeq.R could not be found. So then I added the absolute path to my R script to the command tag. This seemed to work (that is, it got me further, to the next error), but I'm not sure why I had to do this; in all the other tools I'm looking at, the directory to the script to run does not have to be specified; I assumed that the command would run in the appropriate directory. So now I've specified the full path to my R script: command interpreter=bashRscript_wrapper.sh /Users/dtenenba/dev/galaxy-dist/tools/bioc/RNASeq.R $countsTsv $designTsv $organism $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2/command And I get the following long error, which includes all of the output of my R script: Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 133, in run_job job_wrapper.finish( stdout, stderr ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/__init__.py, line 725, in finish self.sa_session.flush() File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/scoping.py, line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py, line 1356, in flush self._flush(objects) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py, line 1434, in _flush flush_context.execute() File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py, line 261, in execute UOWExecutor().execute(self, tasks) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py, line 753, in execute self.execute_save_steps(trans, task) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py, line 768, in execute_save_steps self.save_objects(trans, task) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/unitofwork.py, line 759, in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py, line 1413, in _save_obj c = connection.execute(statement.values(value_params), params) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py, line 824, in execute return Connection.executors[c](self, object, multiparams, params) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py, line 874, in _execute_clauseelement return self.__execute_context(context) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py, line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File /Users/dtenenba/dev/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py, line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters,
Re: [galaxy-dev] Cloud instance connection refused
On Tue, Apr 24, 2012 at 9:16 AM, Hui Zhao zh...@cbio.mskcc.org wrote: Hi, This is Julia from Memorial SLoan-Kettering Cancer Center. I've been using the galaxy Cloudman instance last year and it worked fine. But today when I tried to launch instance galaxy-cloudman-2011-03-22(ami-da58aab3). After the instance was running, it gave me tcp_error: A communication error occurred: Connection refused. Any ideas? Sounds like maybe a security group problem. Did you set up your security group as described here: http://wiki.g2.bx.psu.edu/Admin/Cloud Search for Add Inbound Rules. Dan Thanks a lot, Julia ___ 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/ ___ 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/
