How to count the number of Workflow steps?
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all "HideDatasetAction*" for each tools "post_job_actions" to figure out the total number of steps that will be run. "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionoutput_suppressed_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_l" }, "HideDatasetActionoutput_suppressed_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_r" }, "HideDatasetActionoutput_unmapped_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_l" }, "HideDatasetActionoutput_unmapped_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_r" } }, In the latest galaxy, there no longer seems to be any "HideDatasetAction*" in each tools "post_job_actions" options. How does Galaxy know which output files for a tool it should show or process? Does it have to do something with "RenameDatasetAction*"? "post_job_actions": { "RenameDatasetActionoutput_file": { "action_arguments": { "newname": "19_output_file" }, "action_type": "RenameDatasetAction", "output_name": "output_file" } }, Any guidance would be much appreciated. Thanks,
Manually adding "HideDatasetActions" via the right panel in the editor was deprecated a while back in favor of the workflow output 'asterisks' you see rendered on each step in the workflow editor, but they're still used behind the scenes. When you flag a step as an output, all other non-output steps should have HideDatasetActions added to the step automatically. -Dannon On Tue, Mar 5, 2013 at 5:32 PM, Richard Park <rpark@bu.edu> wrote:
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all "HideDatasetAction*" for each tools "post_job_actions" to figure out the total number of steps that will be run.
"post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionoutput_suppressed_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_l" }, "HideDatasetActionoutput_suppressed_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_r" }, "HideDatasetActionoutput_unmapped_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_l" }, "HideDatasetActionoutput_unmapped_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_r" } },
In the latest galaxy, there no longer seems to be any "HideDatasetAction*" in each tools "post_job_actions" options. How does Galaxy know which output files for a tool it should show or process?
Does it have to do something with "RenameDatasetAction*"?
"post_job_actions": { "RenameDatasetActionoutput_file": { "action_arguments": { "newname": "19_output_file" }, "action_type": "RenameDatasetAction", "output_name": "output_file" } },
Any guidance would be much appreciated. Thanks,
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Hi Dannon, Thanks for the response. If there is a "RenameDatasetActionoutput_file" post job action, does that implicity mean that all other output files are considered HideDatasetActions? thanks, Richard On Tue, Mar 5, 2013 at 6:36 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Manually adding "HideDatasetActions" via the right panel in the editor was deprecated a while back in favor of the workflow output 'asterisks' you see rendered on each step in the workflow editor, but they're still used behind the scenes. When you flag a step as an output, all other non-output steps should have HideDatasetActions added to the step automatically.
-Dannon
On Tue, Mar 5, 2013 at 5:32 PM, Richard Park <rpark@bu.edu> wrote:
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all "HideDatasetAction*" for each tools "post_job_actions" to figure out the total number of steps that will be run.
"post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionoutput_suppressed_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_l" }, "HideDatasetActionoutput_suppressed_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_r" }, "HideDatasetActionoutput_unmapped_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_l" }, "HideDatasetActionoutput_unmapped_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_r" } },
In the latest galaxy, there no longer seems to be any "HideDatasetAction*" in each tools "post_job_actions" options. How does Galaxy know which output files for a tool it should show or process?
Does it have to do something with "RenameDatasetAction*"?
"post_job_actions": { "RenameDatasetActionoutput_file": { "action_arguments": { "newname": "19_output_file" }, "action_type": "RenameDatasetAction", "output_name": "output_file" } },
Any guidance would be much appreciated. Thanks,
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No, rename is a completely separate and unrelated action. Back to your original question, for counting the number of steps, can you just look at the api/workflows/<id> and look at the steps dict? Anything with a tool_id is a tool step. -Dannon On Tue, Mar 5, 2013 at 10:52 PM, Richard Park <rpark@bu.edu> wrote:
Hi Dannon, Thanks for the response. If there is a "RenameDatasetActionoutput_file" post job action, does that implicity mean that all other output files are considered HideDatasetActions? thanks, Richard
On Tue, Mar 5, 2013 at 6:36 PM, Dannon Baker <dannon.baker@gmail.com>wrote:
Manually adding "HideDatasetActions" via the right panel in the editor was deprecated a while back in favor of the workflow output 'asterisks' you see rendered on each step in the workflow editor, but they're still used behind the scenes. When you flag a step as an output, all other non-output steps should have HideDatasetActions added to the step automatically.
-Dannon
On Tue, Mar 5, 2013 at 5:32 PM, Richard Park <rpark@bu.edu> wrote:
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all "HideDatasetAction*" for each tools "post_job_actions" to figure out the total number of steps that will be run.
"post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionoutput_suppressed_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_l" }, "HideDatasetActionoutput_suppressed_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_r" }, "HideDatasetActionoutput_unmapped_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_l" }, "HideDatasetActionoutput_unmapped_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_r" } },
In the latest galaxy, there no longer seems to be any "HideDatasetAction*" in each tools "post_job_actions" options. How does Galaxy know which output files for a tool it should show or process?
Does it have to do something with "RenameDatasetAction*"?
"post_job_actions": { "RenameDatasetActionoutput_file": { "action_arguments": { "newname": "19_output_file" }, "action_type": "RenameDatasetAction", "output_name": "output_file" } },
Any guidance would be much appreciated. Thanks,
___________________________________________________________ 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:
Hi, I'm trying to load an instance of Galaxy from scratch, and I'm getting this error message after configuration and typing "./run.sh": Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/spin1/users/galaxy/galaxy1/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/spin1/users/galaxy/galaxy1/lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/spin1/users/galaxy/galaxy1/lib/galaxy/webapps/galaxy/buildapp.py", line 18, in <module> from galaxy import config, jobs, util, tools File "/spin1/users/galaxy/galaxy1/lib/galaxy/jobs/__init__.py", line 15, in <module> from galaxy import util, model File "/spin1/users/galaxy/galaxy1/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/spin1/users/galaxy/galaxy1/lib/galaxy/datatypes/registry.py", line 9, in <module> import gmap # added for gmap tools ImportError: No module named gmap What is missing? David Hoover Helix Systems Staff
Is this a fresh clone from galaxy-dist or have you pulled it from somewhere else? It looks like your galaxy clone's lib/galaxy/datatypes/registry.py has been altered to have an extra import, 'gmap', for gmap tools. -Dannon On Wed, Mar 6, 2013 at 12:08 PM, David Hoover <hooverdm@helix.nih.gov>wrote:
Hi,
I'm trying to load an instance of Galaxy from scratch, and I'm getting this error message after configuration and typing "./run.sh":
Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**serve.py", line 1062, in invoke exit_code = runner.run(args) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**serve.py", line 227, in run result = self.command() File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**serve.py", line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_**type, name, global_conf) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 561, in get_context section) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/util/pastescript/**loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.**parse("x=" + s).load(False) File "/spin1/users/galaxy/galaxy1/**lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/spin1/users/galaxy/galaxy1/**lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/spin1/users/galaxy/galaxy1/**lib/galaxy/webapps/galaxy/**buildapp.py", line 18, in <module> from galaxy import config, jobs, util, tools File "/spin1/users/galaxy/galaxy1/**lib/galaxy/jobs/__init__.py", line 15, in <module> from galaxy import util, model File "/spin1/users/galaxy/galaxy1/**lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/spin1/users/galaxy/galaxy1/**lib/galaxy/datatypes/registry.**py", line 9, in <module> import gmap # added for gmap tools ImportError: No module named gmap
What is missing?
David Hoover Helix Systems Staff ______________________________**_____________________________ 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:
This is a fresh clone, from galaxy-dist, but I have a pile of patch files to keep my local hacks straight. I forgot about the registry.py file. Removed that, as well as the blast import. It's hard to keep local hacks and regular updates in sync... Thanks, David On 3/6/2013 12:16 PM, Dannon Baker wrote:
Is this a fresh clone from galaxy-dist or have you pulled it from somewhere else? It looks like your galaxy clone's lib/galaxy/datatypes/registry.py has been altered to have an extra import, 'gmap', for gmap tools.
-Dannon
On Wed, Mar 6, 2013 at 12:08 PM, David Hoover <hooverdm@helix.nih.gov <mailto:hooverdm@helix.nih.gov>> wrote:
Hi,
I'm trying to load an instance of Galaxy from scratch, and I'm getting this error message after configuration and typing "./run.sh":
Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/spin1/users/galaxy/galaxy1/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/spin1/users/galaxy/galaxy1/lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/spin1/users/galaxy/galaxy1/lib/galaxy/webapps/galaxy/buildapp.py", line 18, in <module> from galaxy import config, jobs, util, tools File "/spin1/users/galaxy/galaxy1/lib/galaxy/jobs/__init__.py", line 15, in <module> from galaxy import util, model File "/spin1/users/galaxy/galaxy1/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/spin1/users/galaxy/galaxy1/lib/galaxy/datatypes/registry.py", line 9, in <module> import gmap # added for gmap tools ImportError: No module named gmap
What is missing?
David Hoover Helix Systems Staff ___________________________________________________________ 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:
I've installed the latest version of galaxy, and the admin column won't scroll. I can't see any of the toolshed functions unless mybrowser is expanded beyond the size of my desktop display. Is there something wrong? David Hoover Helix Systems Staff
participants (3)
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Dannon Baker
-
David Hoover
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Richard Park