Re: [galaxy-dev] Getting tool dirpath in a Python code file
On Thu, Apr 14, 2011 at 2:08 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, I have a tool with a code file=my_script.py/ tag and in that code file I'm trying to get the tool dirpath where that script and the tool XML exist. I've tried: os.path.abspath(os.path.dirname(sys.argv[0])) os.path.abspath(os.path.dirname(__file__)) And both don't work as expected. Is there a galaxy class I could import which will have the tool directory path? regards, Leandro For standard Python tools in Galaxy, I'm using os.path.split(sys.argv[0])[0] to get the path, which on reflection probably should be written as os.path.dirname(sys.argv[0]) as you suggest. What do __file__ and sys.argv[0] give you? The simplest way to debug this is to add a print statement, since Galaxy will show the stdout. 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/
Re: [galaxy-dev] Error when trying to download workflow
I could narrow it down even further. As soon as I set anything to To be
set at runtime the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a
screenshot of a really simple workflow whose download fails. I recreated
the workflow at the public instance at http://main.g2.bx.psu.edu and
shared it with you. There the download also fails for me.
Best regards,
Sarah
On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not,
you'll have to do some debugging yourself. Here are some things you
might try:
*on your local instance, try exporting simpler workflows and seeing if
there's a tool or configuration that does or does work.
*on our public instance, try creating a workflow identical to the one
that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance
that I have access to, I can probably fix it.
Thanks,
J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the
workflow still does not work. The error is the same.
Best regards,
Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export
it successfully, so updating your Galaxy instance may solve your
problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists
rather than individual galaxy developers for community and archival
purposes; I've cc'd this one to galaxy-dev.
Thanks,
J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the
galaxy-dev list
(http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html)
when trying to download a workflow.
Were you able to find a solution or are you still working on it? I
attached a screenshot of the workflow (like you also requested on
the list). Let me know if I can provide you with any additional
details to help with the debugging.
Best regards,
Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] GET
/workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1 500 -
http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07;
Mozilla/5.0
(X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322
fil
e:///home/diehl/Pictures/Screenshot.png
Fedora/3.6.16-1.fc14 Firefox/3.6.16
Error -type 'exceptions.TypeError': 'WorkflowStep' object is
unsubscriptable
URL:
http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line
80 in __call__
return self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line
145 in __call__
body = method( trans, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
line 74 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ),
indent=4, sort_keys=True )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1078 in export_to_file
stored_dict = self._workflow_to_dict( trans, stored )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1571 in _workflow_to_dict
step['inputs'].append( { name : name, description : runtime
parameter for tool %s % module.get_name() } )
TypeError: 'WorkflowStep' object is unsubscriptable
Screenshot.png
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___
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 when trying to download workflow
Thanks Sarah. I was having trouble reproducing because I hadn't set a runtime
parameter. I've fixed the bug in galaxy-central changeset 5387:835656900dd0 ;
after making this change, I was able to successfully export and import
workflows with runtime parameters.
Best,
J.
On Apr 14, 2011, at 10:01 AM, Sarah Diehl wrote:
I could narrow it down even further. As soon as I set anything to To be set
at runtime the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a
screenshot of a really simple workflow whose download fails. I recreated
the workflow at the public instance at http://main.g2.bx.psu.edu and
shared it with you. There the download also fails for me.
Best regards,
Sarah
On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not,
you'll have to do some debugging yourself. Here are some things you
might try:
*on your local instance, try exporting simpler workflows and seeing if
there's a tool or configuration that does or does work.
*on our public instance, try creating a workflow identical to the one
that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance
that I have access to, I can probably fix it.
Thanks,
J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the
workflow still does not work. The error is the same.
Best regards,
Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export
it successfully, so updating your Galaxy instance may solve your
problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists
rather than individual galaxy developers for community and archival
purposes; I've cc'd this one to galaxy-dev.
Thanks,
J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the
galaxy-dev list
(http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html)
when trying to download a workflow.
Were you able to find a solution or are you still working on it? I
attached a screenshot of the workflow (like you also requested on
the list). Let me know if I can provide you with any additional
details to help with the debugging.
Best regards,
Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] GET
/workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1 500 -
http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07;
Mozilla/5.0
(X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322
fil
e:///home/diehl/Pictures/Screenshot.png
Fedora/3.6.16-1.fc14 Firefox/3.6.16
Error -type 'exceptions.TypeError': 'WorkflowStep' object is
unsubscriptable
URL:
http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line
80 in __call__
return self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line
145 in __call__
body = method( trans, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
line 74 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ),
indent=4, sort_keys=True )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1078 in export_to_file
stored_dict = self._workflow_to_dict( trans, stored )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1571 in _workflow_to_dict
step['inputs'].append( { name : name, description : runtime
parameter for tool %s % module.get_name() } )
TypeError: 'WorkflowStep' object is unsubscriptable
Screenshot.png
___
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/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Re: [galaxy-dev] Error when adding datasets
I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and reply back with the output of the debug statements. Assuming you start your Galaxy instance with: sh run.sh you'll see the results of the debug statements in the log scrolling in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think this issue is related to the Galaxy eggs, but instead looks like a data issue of some kind. Please replly back with answers to the following questions. How did you create your database? Couldn't have done it more simply ^^: CREATE DATABASE galaxy_db; GRANT ALL ON DATABASE galaxy_db TO galaxy; executed in psql. The very same way I did for the one that's still working fine. Did you populate it with any data exported from another database? In the beginning yes but when I saw that error I dropped the database and re-created it again, to start anew and test on an empty database. I even created a brand new test database to see if the issue wasn't related to stuff remaining after dropping the database, but it turned out badly too. What version of Galaxy are you using? The latest dist, cause when I saw how things were turning out I hg pulled and updated hoping it would fix the issue. I did that this morning. What database are you using? PostgreSQL, as recommended in the doc. Greg Von Kuster Cheers, L-A On Apr 14, 2011, at 5:38 AM, Louise-Amélie Schmitt wrote: Hello everyone I have an issue when trying to import new datasets or when putting a dataset into a history. I saw Edward Kirton had the same problem but he got no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html Here is the error message I get when clicking the Add datasets button in a library, in the admin's Manage data libraries panel: UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped URL: http://manni/galaxy/library_common/upload_library_dataset?library_id=f2db41e1fa331b3eshow_deleted=Falsecntrller=library_adminfolder_id=f2db41e1fa331b3euse_panels=False File '/g/funcgen/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/g/funcgen/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py', line 109 in __call__ return self.app( environ, start_response ) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/g/funcgen/galaxy/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/g/funcgen/galaxy/lib/galaxy/web/controllers/library_common.py', line 907 in upload_library_dataset trans.sa_session.refresh( history ) File '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py', line 127 in do return getattr(self.registry(), name)(*args, **kwargs) File '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py', line 925 in refresh raise
[galaxy-dev] Trouble setting up Galaxy with apache proxy
I used this step by step : https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy to set up galaxy with apache proxy. I added these lines to httpd.conf file : RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/bioinfo/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/bioinfo/galaxy/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:7070$1 [P] And these ones to universe_wsgi.ini : [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy I face a problem with the history panel which always displays : Your history is empty. Click 'Get Data' on the left pane to start . Even if I upload Data, even if I log into galaxy. Here is an output of galaxy logs : 195.221.174.200 - - [13/Apr/2011:16:38:56 +0200] GET /galaxy/tool_runner?tool_id=upload1 HTTP/1.1 200 - http://marmadais.cirad.fr:7070/galaxy/root/tool_menu; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:2.0) Gecko/20100101 Firefox/4.0 galaxy.web.framework DEBUG 2011-04-13 16:39:04,250 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create 195.221.174.200 - - [13/Apr/2011:16:39:04 +0200] POST /galaxy/tool_runner/upload_async_create HTTP/1.1 500 - http://marmadais.cirad.fr:7070/galaxy/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:2.0) Gecko/20100101 Firefox/4.0 Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'id' URL: http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/ errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.p y', line 80 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexcepti ons.py', line 632 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 65 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py' , line 212 in upload_async_create errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1192 in update_state value, error = check_param( trans, input, incoming_value, context ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 56 in check_param value = param.from_html( value, trans, param_values ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 638 in from_html legal_values = self.get_legal_values( trans, context ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 808 in get_legal_values return set( dbkey for dbkey, _ in trans.db_builds ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 695 in db_builds .filter_by( deleted=False, history_id=self.history.id, extension=len ) AttributeError: 'NoneType' object has no attribute 'id' Any help welcome. Thankx. ___ 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 when adding datasets
On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you. galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans: galaxy.web.framework.GalaxyWebUITransaction object at 0x29f40950 galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans.sa_session: sqlalchemy.orm.scoping.ScopedSession object at 0x19ab21d0 Thanks again L-A Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and reply back with the output of the debug statements. Assuming you start your Galaxy instance with: sh run.sh you'll see the results of the debug statements in the log scrolling in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think this issue is related to the Galaxy eggs, but instead looks like a data issue of some kind. Please replly back with answers to the following questions. How did you create your database? Couldn't have done it more simply ^^: CREATE DATABASE galaxy_db; GRANT ALL ON DATABASE galaxy_db TO galaxy; executed in psql. The very same way I did for the one that's still working fine. Did you populate it with any data exported from another database? In the beginning yes but when I saw that error I dropped the database and re-created it again, to start anew and test on an empty database. I even created a brand new test database to see if the issue wasn't related to stuff remaining after dropping the database, but it turned out badly too. What version of Galaxy are you using? The latest dist, cause when I saw how things were turning out I hg pulled and updated hoping it would fix the issue. I did that this morning. What database are you using? PostgreSQL, as recommended in the doc. Greg Von Kuster Cheers, L-A On Apr 14, 2011, at 5:38 AM, Louise-Amélie Schmitt wrote: Hello everyone I have an issue when trying to import new datasets or when putting a dataset into a history. I saw Edward Kirton had the same problem but he got no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html Here is the error message I get when clicking the Add datasets button in a library, in the admin's Manage data libraries panel: UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped URL: http://manni/galaxy/library_common/upload_library_dataset?library_id=f2db41e1fa331b3eshow_deleted=Falsecntrller=library_adminfolder_id=f2db41e1fa331b3euse_panels=False File '/g/funcgen/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File
[galaxy-dev] script to download genomes
Hello, I'm working on a simple python script that auto-magically creates all indexes, and pre-processing necessary to add a genome to galaxy. I was wondering if anyone had a script to download all the genomes that are presented to you in the default genome drop down box? Also I'm not to confident about what all preprocessing actually is (with respect to the default configuration). So far I create the create indexes for the following tools and add their appropriate entry into their tools-data config file: sam index bowtie, base/color bwa, base/color bfast, base (any advice on how to do color?) blast (n and p) Am I missing any tool that requires preprocessing? Thanks, James ___ 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] Bowtie why it does not take the 1_sequence.txt nor for bowtie nor the Convert
Dear Sir I try to use Bowtie mapping in galaxy , I import my Illumina s_1_sequence.txt , then I try to use the convert my userName is my email 21: FASTQ Groomer on data 9 An error occurred running this job: /There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have/ but I do have for all the files an error I upload the data using URL http://home.adm.unige.ch/~prnfg/HowardRiezman/wt(RH%20448)%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-1B%20erg3%209f-10A-1B%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-9D%20erg3%2013f-9D-9D%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/13f-13B%20erg3%2013f-9D-13B%20%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/erg3%20RH%205702%20erg3%20s_1_sequence.txt http://home.adm.unige.ch/~prnfg/HowardRiezman/9f-3A%20erg3%209f-10A-3A%20s_1_sequence.txt Could you advice me ? Best regards ___ 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] NLStradamus wrapper (for nuclear localization signals)
Hi all, I just wanted to mention (to avoid duplicate work) that I have a working Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear localization signals (NLSs) from a protein FASTA file. The wrapper does a little reformatting of the output to get a clean tabular file for use in Galaxy. I would release this to the Galaxy Tool Shed now, but the tool's author Alex Nguyen Ba tells me he hopes to have an update released fairly soon which should include a native tabular output - probably with a richer column structure. So rather than having to change the tool output and potentially break workflows, I plan to wait till then. However, if anyone wants the wrapper before then, drop me an email. Regards, Peter References: A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics. 2009 Jun 29;10(1):202. http://www.moseslab.csb.utoronto.ca/NLStradamus ___ 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 when adding datasets
The thing is, we use LDAP logging so we can't even access the website without logging in. Moreover, when I logged in, I arrived on the data analysis page where the automatic unnamed history was obviously created in the history panel. I forgot to mention we have issues creating and deleting histories, like, we can't access some histories and everytime we delete histories, two extra unnamed histories are created. As I mentioned before, it is also impossible to load a dataset in any history, existing or not. Do you think it could be linked to our using LDAP? Thanks L-A On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kuster g...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you. galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans: galaxy.web.framework.GalaxyWebUITransaction object at 0x29f40950 galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans.sa_session: sqlalchemy.orm.scoping.ScopedSession object at 0x19ab21d0 Thanks again L-A Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and reply back with the output of the debug statements. Assuming you start your Galaxy instance with: sh run.sh you'll see the results of the debug statements in the log scrolling in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think this issue is related to the Galaxy eggs, but instead looks like a data issue of some kind. Please replly back with answers to the following questions. How did you create your database? Couldn't have done it more simply ^^: CREATE DATABASE galaxy_db; GRANT ALL ON DATABASE galaxy_db TO galaxy; executed in psql. The very same way I did for the one that's still working fine. Did you populate it with any data exported from another database? In the beginning yes but when I saw that error I dropped the database and re-created it again, to start anew and test on an empty database. I even created a brand new test database to see if the issue wasn't related to stuff remaining after dropping the database, but it turned out badly too. What version of Galaxy are you using? The latest dist, cause when I saw how things were turning out I hg pulled and updated hoping it would fix the issue. I did that this morning. What database are you using? PostgreSQL, as recommended in the doc. Greg Von Kuster Cheers, L-A On Apr 14, 2011, at 5:38 AM, Louise-Amélie Schmitt wrote: Hello everyone I have an issue when trying to import new datasets or when putting a dataset into a history. I saw Edward Kirton had the same problem but he got no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html Here is the error message I get when clicking the Add datasets button in a library, in the admin's Manage data libraries panel: UnmappedInstanceError: Class '__builtin__.NoneType' is not
Re: [galaxy-dev] Error when adding datasets
Hello Louise, I've CC'd Nate on this as he may be able to help - although no guarantees. I'm not expert enough in this area to know where to look for the cause. Perhaps someone in the community can help as well. It is likely that LDAP is playing a role in this behavior. On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote: The thing is, we use LDAP logging so we can't even access the website without logging in. Moreover, when I logged in, I arrived on the data analysis page where the automatic unnamed history was obviously created in the history panel. I forgot to mention we have issues creating and deleting histories, like, we can't access some histories and everytime we delete histories, two extra unnamed histories are created. As I mentioned before, it is also impossible to load a dataset in any history, existing or not. Do you think it could be linked to our using LDAP? Thanks L-A On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kuster g...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you registered normally, a history would have been automatically created for you. But somehow you don't have a history - no idea why / how this happened, but it is very unlikely this is a result of a bug within Galaxy. Try logging out and logging in again and a new history should be created for you. galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans: galaxy.web.framework.GalaxyWebUITransaction object at 0x29f40950 galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### trans.sa_session: sqlalchemy.orm.scoping.ScopedSession object at 0x19ab21d0 Thanks again L-A Le jeudi 14 avril 2011 à 11:05 -0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new database, and they would all be empty. When you first registered as the admin user, it would have automatically populated several tables with data, including the history table. One or more of these things must not have been successful. To attempt to narrow down the problem, I'll need you to do the following. Here are lines # 905 - 907 in ~/lib/galaxy/web/controllers/library-common.py # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() trans.sa_session.refresh( history ) Please add the following debug statements: # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() log.debug(### history: %s % str( history )) log.debug(### trans: %s % str( trans )) log.debug(### trans.sa_session: %s % str( trans.sa_session )) trans.sa_session.refresh( history ) Stop and restart your Galaxy server after making the above changes, and reply back with the output of the debug statements. Assuming you start your Galaxy instance with: sh run.sh you'll see the results of the debug statements in the log scrolling in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think this issue is related to the Galaxy eggs, but instead looks like a data issue of some kind. Please replly back with answers to the following questions. How did you create your database? Couldn't have done it more simply ^^: CREATE DATABASE galaxy_db; GRANT ALL ON DATABASE galaxy_db TO galaxy; executed in psql. The very same way I did for the one that's still working fine. Did you populate it with any data exported from another database? In the beginning yes but when I saw that error I dropped the database and re-created it again, to start anew and test on an empty database. I even created a brand new test database to see if the issue wasn't related to stuff remaining after dropping the database, but it turned out badly too. What version of Galaxy are you using? The latest dist, cause when I saw how things were turning out I hg pulled and updated hoping it would fix the issue. I did that this morning. What database are you using? PostgreSQL, as recommended in the doc. Greg Von Kuster Cheers, L-A On Apr 14, 2011, at 5:38 AM, Louise-Amélie Schmitt wrote: Hello everyone I have an issue when trying to import new datasets or when putting a
[galaxy-dev] Workflow variables and the workflow API
I'm working on a module that involves calling a workflow multiple times over a
set of data.
The workflow has a variable that I use for renaming output files.
I see, using the workflow_execute.py example how to pass in file names, but I
don't see how to pass in a value for this variable.
When I do a ./display.py api key
http://jaxgalaxydev01/api/workflows/workflow id I see the two input data
files I would expect, but I don't see this variable.
ex:
Member Information
--
url: /api/workflows/workflow id
inputs: {'207': {'value': '', 'label': 'Input Dataset'}, '211': {'value': '',
'label': 'Input Dataset'}}
id: workflow id
name: Single-end RNA Seq with grooming v 2.0 (imported from uploaded file)
Is there anyway to get at this variable so I can set it when I call a workflow
through the API?
Thanks,
Dave
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Re: [galaxy-dev] script to download genomes
James; I'm working on a simple python script that auto-magically creates all indexes, and pre-processing necessary to add a genome to galaxy. I was wondering if anyone had a script to download all the genomes that are presented to you in the default genome drop down box? Really great you are interested in this are. We've been working on this problem as part of the cloudbiolinux project: https://github.com/chapmanb/cloudbiolinux and have a fabric install file: https://github.com/chapmanb/cloudbiolinux/blob/master/data_fabfile.py the pulls genomes and index types specified by a configuration file: https://github.com/chapmanb/cloudbiolinux/blob/master/config/biodata.yaml This has two ways of installing the indexes. The first, install_data, will download the genomes from UCSC/Ensembl/NCBI and then build the indexes locally. The second, install_data_s3, has pre-prepared and indexed genomes stored in Amazon S3 buckets. This lets you fetch and unpack ready to go genomes without having the overhead of indexing; this works from anywhere -- local or Amazon cloud machines. After download, both methods update the appropriate *.loc files to integrate with Galaxy. As you mentioned, there are a lot of different targets and genomes, and we're definitely interested in expanding out to include them. It sounds like this approach is similar to what you were working on. If you're interested, we'd be very happy to have you involved. We've been working with Enis on this but it's not an official Galaxy team project; rather it's a community supplement to the great install automation they already provide. Hope this helps, Brad ___ 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/
