User: yychangsd

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yychangsd30
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30
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New User
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Last seen:
4 months, 3 weeks ago
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1 year, 4 months ago
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y********@gmail.com

Posts by yychangsd

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galaxy start error
... I installed a local galaxy and start it successfully. Then I'd like to add some pipelines into my local galaxy. It was running well. I'd like to shut down and re-start it and got an error like this: Activating virtualenv at .venv Requirement already satisfied: pip>=8.1 in ./.venv/lib/ ...
galaxy written 5 months ago by yychangsd30 • updated 4 months ago by danielsauceda60
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local galaxy instance sqlite3.OperationError
... Hi, I'd like to install a local galaxy. After git clone the release_17.0, I use sh run.sh to start the galaxy. But I got an error like this: migrate.versioning.repository DEBUG 2017-05-19 09:41:03,875 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository ...
galaxy written 6 months ago by yychangsd30
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(Closed) qiime warning or error
... I installed qiime. And run the pick_open_reference_otus.py I got this: "version is 2.1\n".format(ver=ver), UserWarning) /usr/local/lib/python2.7/dist-packages/pandas/computation/__init__.py:25: UserWarning: The installed version of numexpr 2.0.1 is not supported in pandas and will be no ...
software error written 14 months ago by yychangsd30
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How to differentiate two different galaxies running on the same server
... I installed 2 galaxy instances in my cluster. One is for internal use, and the other is public. When I use `ps aux | grep galaxy` to check the status, it shows the exact output. root 8483 3.1 1.8 1613920 277456 ? Sl Sep25 544:23 python ./scripts/paster.py serve config/galaxy.ini -- ...
galaxy local multiple-instances admin written 14 months ago by yychangsd30 • updated 14 months ago by Jennifer Hillman Jackson23k
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Reporting output tracks FAILED in tophat
... I got an error from topcoat. Any suggestions would be appreciated~~ Thanks~ [2016-09-19 16:33:04] Beginning TopHat run (v2.0.12) ----------------------------------------------- [2016-09-19 16:33:04] Checking for Bowtie Bowtie version: 2.1.0.0 [2016-09-19 16:33:04] ...
local job tophat error written 15 months ago by yychangsd30 • updated 15 months ago by Jennifer Hillman Jackson23k
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an error occurred while getting updates from server.
... I persistently got this error from my local galaxy instance. Any idea about it? thanks so much~~ { "agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/601.7.7 (KHTML, like Gecko) Version/9.1.2 Safari/601.7.7", "url": "http://52.34.123.54:8080/api/histories/1c ...
permissions local galaxy admin written 15 months ago by yychangsd30 • updated 15 months ago by Jennifer Hillman Jackson23k
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Dataset generation errors
... I got an error when running my local galaxy instance. Dataset generation errors Dataset 39: workflow output Tool execution generated the following error message: Fatal error: Matched on error Thu Sep 15 09:21:40 PDT 2016 Running subset of jobs: qc-pe qc-star-pe can not submit qsub job and retur ...
local galaxy job admin error written 15 months ago by yychangsd30 • updated 15 months ago by Jennifer Hillman Jackson23k
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Comment: C: UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position
... Thanks for your comments. Actually I used this to convert my galaxy_db in mysql: mysql> ALTER DATABASE galaxy_db CHARACTER SET utf8 COLLATE utf8_unicode_ci; Query OK, 1 row affected (0.01 sec) And I also checked job_conf.xml. It seems fine. But I still get this error... ...
written 15 months ago by yychangsd30
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UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 534: ordinal not in range(256)
... My local galaxy instance is connected with mysql. When I run a job I get an error: Traceback (most recent call last): File "/home/oasis/data/galaxy-new/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/oasis/data/galaxy-new/lib/ ...
unicode local jobs admin error written 15 months ago by yychangsd30 • updated 15 months ago by Jennifer Hillman Jackson23k
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ftp link does not work
... Finally I set up proftpd for my local galaxy instance. I also set up anonymous log in for this ftp. I can log into ftp in terminal, but can not access it through ftp://localhost. Any suggestions about it? Thanks~ ...
url local galaxy ftp written 15 months ago by yychangsd30 • updated 15 months ago by Jennifer Hillman Jackson23k

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