Hi all, I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting: $ sh scripts/cleanup_datasets/delete_userless_histories.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> import sqlalchemy as sa ImportError: No module named sqlalchemy We have relatively limited space on our storage server, so it's imperative that I be able to execute these scripts and be able to clean up deleted material. I welcome any suggestions. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
Hi Scott, The quick fix is to source your virtualenv first and you should be good to go. -Dannon On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,
I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting:
$ sh scripts/cleanup_datasets/delete_userless_histories.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> import sqlalchemy as sa ImportError: No module named sqlalchemy
We have relatively limited space on our storage server, so it's imperative that I be able to execute these scripts and be able to clean up deleted material. I welcome any suggestions.
Best regards,
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Dannon, That absolutely did the trick. Thanks so much for your assistance. Best, Scott On Fri, May 20, 2016 at 9:11 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hi Scott,
The quick fix is to source your virtualenv first and you should be good to go.
-Dannon
On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi <Scott.B.Szakonyi.1@nd.edu> wrote:
Hi all,
I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting:
$ sh scripts/cleanup_datasets/delete_userless_histories.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> import sqlalchemy as sa ImportError: No module named sqlalchemy
We have relatively limited space on our storage server, so it's imperative that I be able to execute these scripts and be able to clean up deleted material. I welcome any suggestions.
Best regards,
-- Scott B. Szakonyi Research Programmer
*Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
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Scott Szakonyi