Question: how to clean the current library
0
gravatar for biowz
2.3 years ago by
biowz0
United States
biowz0 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! 

ADD COMMENTlink modified 2.3 years ago by Bjoern Gruening4.8k • written 2.3 years ago by biowz0
1
gravatar for Bjoern Gruening
2.3 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi,

please have a look at the following script:

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

Hope this helps,

Bjoern

ADD COMMENTlink written 2.3 years ago by Bjoern Gruening4.8k

 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 REPLYlink written 2.3 years ago by biowz0

Why do you need this?

ADD REPLYlink written 2.3 years ago by Bjoern Gruening4.8k

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 REPLYlink written 2.3 years ago by biowz0

Are you running it inside your galaxy root dir?

ADD REPLYlink written 2.3 years ago by Bjoern Gruening4.8k

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 REPLYlink written 2.3 years ago by biowz0
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