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Question: how to clean the current library
0
gravatar for biowz
3.3 years ago by
biowz • 0
United States
biowz • 0 wrote:

I used local galaxy to run data. However I deleted the current library. but I think this still occupied my disk volume. I  want to clean them totally, how  I can do it?

Thank you very much in advance! 
current library local galaxy • 796 views
ADD COMMENT • link •
modified 3.3 years ago by Bjoern Gruening ♦ 5.1k • written 3.3 years ago by biowz • 0
1
gravatar for Bjoern Gruening
3.3 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

please have a look at the following script:

python ./scripts/cleanup_datasets/cleanup_datasets.py --help

Hope this helps,

Bjoern
ADD COMMENT • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

 Hi Bjoern,

First  I added the following sentences in  cleanup_datasets.py from" ./ scripts/cleanup_datasets/cleanup_datasets.py"

GALAXY_LIB="/Users/biowzmailustceducn/galaxy/lib"

if [ "$GALAXY_LIB" != "/Users/biowzmailustceducn/galaxy/lib" ]: then

    if [ -n "$PYTHONPATH" ]: then

        export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"

    else

        export PYTHONPATH="$GALAXY_LIB"

    fi

fi

And next

python /Users/biowzmailustceducn/galaxy/scripts/cleanup_datasets/cleanup_datasets.py 

The error occurs as following

File "/Users/biowzmailustceducn/galaxy/scripts/cleanup_datasets/cleanup_datasets.py", line 6

    if [ -n "$PYTHONPATH" ]: then

    ^

IndentationError: unexpected indent

Would  you like to help me solve this problem? Thank you very much for your help!

Best wishes

Hil

ADD REPLY • link written 3.3 years ago by biowz • 0

Why do you need this?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

If I just run this code, the errors like this as following:

Traceback (most recent call last):

  File "/Users/biowzmailustceducn/galaxy/scripts/cleanup_datasets/cleanup_datasets.py", line 14, in <module>

    from galaxy import eggs

ImportError: No module named galaxy

Would you like to help us about this?

ADD REPLY • link written 3.3 years ago by biowz • 0

Are you running it inside your galaxy root dir?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Thank you very much! I pasted this file under galaxy root dir, but I met another question,as follow:

Traceback (most recent call last):

  File "./cleanup_datasets.py", line 531, in <module>

    if __name__ == "__main__": main()

  File "./cleanup_datasets.py", line 101, in main

    for key, value in config_parser.items( "app:main" ):

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ConfigParser.py", line 642, in items

    raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'

ADD REPLY • link written 3.3 years ago by biowz • 0
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