Micropathology
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| Hello |
Micropathology
/ gist:13a127540f4577184976a6fb505a31b6
Created
March 17, 2018 12:54
Install of refseqmasher
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| Fetching package metadata ................. | |
| Solving package specifications: | |
| PackageNotFoundError: Packages missing in current channels: | |
| - refseq_masher 0.1.1* -> mash >=2.0 -> capnproto | |
| - refseq_masher 0.1.1* -> mash >=2.0 -> gsl 1.16* | |
| We have searched for the packages in the following channels: | |
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| [server:main] | |
| use = egg:Paste#http | |
| use_threadpool = True | |
| host = 127.0.0.1 | |
| port = 8080 | |
| [filter:proxy-prefix] | |
| use = egg:PasteDeploy#prefix | |
| [filter:gzip] |
Micropathology
/ gist:4ce9eac0a90e4eb09208cd1650b13f91
Last active
March 20, 2018 11:53
Galaxy log 20/03/18
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| CloudMan from Galaxy | |
| Admin | Report bugs | Wiki | Screencast | |
| The entire log file (/mnt/galaxy/galaxy-app/main.log) is shown. Show latest | Back to admin view | |
| galaxy.queue_worker INFO 2018-03-20 10:27:44,664 Initializing main Galaxy Queue Worker on sqlalchemy+postgres://galaxy@localhost:5930/galaxy | |
| tool_shed.tool_shed_registry DEBUG 2018-03-20 10:27:44,712 Loading references to tool sheds from /mnt/galaxy/galaxy-app/config/tool_sheds_conf.xml | |
| tool_shed.tool_shed_registry DEBUG 2018-03-20 10:27:44,712 Loaded reference to tool shed: Galaxy Main Tool Shed | |
| tool_shed.tool_shed_registry DEBUG 2018-03-20 10:27:44,712 Loaded reference to tool shed: Galaxy Test Tool Shed | |
| galaxy.app DEBUG 2018-03-20 10:27:44,715 Using "galaxy.ini" config file: /mnt/galaxy/galaxy-app/config/galaxy.ini |
Micropathology
/ gist:57318e070a671f84dfcd3146b9186a45
Created
March 20, 2018 15:50
Galaxy log post 4.4 conda
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| CloudMan from Galaxy | |
| Admin | Report bugs | Wiki | Screencast | |
| Only up to the most recent 200 lines of the file (/mnt/galaxy/galaxy-app/main.log) are shown. Show all | Show less | Show more | Back to admin view | |
| galaxy.tools.actions INFO 2018-03-20 15:38:48,061 Handled output named out_fna for tool toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 (16.605 ms) | |
| galaxy.tools.actions INFO 2018-03-20 15:38:48,078 Handled output named out_faa for tool toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 (17.159 ms) | |
| galaxy.tools.actions INFO 2018-03-20 15:38:48,102 Handled output named out_ffn for tool toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 (23.389 ms) | |
| galaxy.tools.actions INFO 2018-03-20 15:38:48,117 Handled output named out_sqn for tool toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 (15.481 ms) | |
| galaxy.tools.actions INFO 2018-03-20 15:38:48,136 Handled output named out_fsa for tool toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 (18.391 ms) |
Micropathology
/ gist:bee4ac9601de5739445c3d3a595b606b
Created
March 30, 2018 12:35
30_03_18_conda_kraken_error
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| galaxy.jobs.handler INFO 2018-03-30 12:31:10,366 (6088) Job dispatched | |
| galaxy.tools.deps DEBUG 2018-03-30 12:31:10,560 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package | |
| galaxy.tools.deps DEBUG 2018-03-30 12:31:10,560 Using dependency kraken version 0.10.6_eaf8fb68 of type conda | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-30 12:31:10,560 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda list --name __kraken@0.10.6_eaf8fb68 --export > /mnt/galaxy/tmp/jobdepsUqR4RTea42a74b7bf23de1655065d377d25493f18569d396a2ca072edc0e3f40d60c43/__kraken@0.10.6_eaf8fb68 | |
| galaxy.tools.deps.conda_util DEBUG 2018-03-30 12:31:10,901 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --unknown --offline --prefix /mnt/galaxy/tmp/job_working_directory/006/6088/conda-env --file /mnt/galaxy/tmp/jobdepsUqR4RTea42a74b7bf23de1655065d377d25493f18569d396a2ca072edc0e3f40d60c43/__kraken@0.10 |
Micropathology
/ gist:3033d8980f5e3209cf289b6cd90674df
Created
July 9, 2018 16:20
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| ---------------------------------------- | |
| Exception happened during processing of request from ('127.0.0.1', 60252) | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread | |
| self.finish_request(request, client_address) | |
| File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request | |
| self.RequestHandlerClass(request, client_address, self) | |
| File "/usr/lib/python2.7/SocketServer.py", line 654, in __init__ | |
| self.finish() | |
| File "/usr/lib/python2.7/SocketServer.py", line 713, in finish |
Micropathology
/ gist:6c4cde4f2ba47035aa1011278205b14f
Created
July 9, 2018 16:24
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| 127.0.0.1 - - [09/Jul/2018:15:57:03 +0000] "GET /galaxy/ HTTP/1.0" 200 - "-" "python-requests/2.18.4" | |
| galaxy.workflow.modules DEBUG 2018-07-09 15:57:06,098 toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1: using version '1.0.2' instead of version '1.0.1' specified in this workflow. | |
| 94.125.130.125 - - [09/Jul/2018:15:57:06 +0000] "POST /galaxy/workflow/upload_import_workflow HTTP/1.0" 500 - "http://34.201.67.187/galaxy/workflow/import_workflow" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/67.0.3396.99 Safari/537.36" | |
| Error - : 'header' | |
| URL: http://34.201.67.187/galaxy/workflow/upload_import_workflow | |
| File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ | |
| app_iter = self.application(environ, sr_checker) | |
| File '/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ | |
| return self.application(environ, start_response) | |
| File '/mnt/galaxy/galaxy-app/.venv/local/lib/python2.7/ |
Micropathology
/ gist:a7bbea886a4b3f88f2670f60faa5dca7
Created
July 10, 2018 12:29
Galaxy-Workflow-Hydra_custom_DEV_pipline_170418v2 (1).ga
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| { | |
| "a_galaxy_workflow": "true", | |
| "annotation": "", | |
| "format-version": "0.1", | |
| "name": "Hydra_custom_DEV_pipline_170418v2", | |
| "steps": { | |
| "0": { | |
| "annotation": "", | |
| "content_id": null, | |
| "errors": null, |
Micropathology
/ gist:513d5f40abcabd36d7be51b7776804ba
Created
July 30, 2018 16:23
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| galaxy.web.stack DEBUG 2018-07-30 16:12:31,741 server_name set to: main | |
| galaxy.queue_worker INFO 2018-07-30 16:12:31,741 Initializing main Galaxy Queue Worker on sqlalchemy+postgres://galaxy@localhost:5930/galaxy | |
| galaxy.app DEBUG 2018-07-30 16:12:31,776 Using "galaxy.ini" config file: /mnt/galaxy/galaxy-app/config/galaxy.ini | |
| Traceback (most recent call last): | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory | |
| app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/app.py", line 84, in __init__ | |
| self._configure_models(check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file) | |
| File "/mnt/galaxy/galaxy-app/lib/galaxy/config.py", line 1120, in _configure_models | |
| create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self) |
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