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qinqian / lisa

epigenome analysis to rank transcription factors
http://lisa.cistrome.org
MIT License
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meta.xls file cannot be found #1

Closed kaltinel closed 4 years ago

kaltinel commented 4 years ago

I am trying to use LISA with my large gene lists. However, I am encountering many errors in the way. I am trying to run it with : lisa_model --sample_number 1 --species hg38 --gene_set /home/data/genename_FC12_DE_DOWN.txt --foreground None --background None --prefix=/home/data --new_h5=None --covariates=None --only_newhdf5=None

And I am receiving an error of : 

File "pandas/_libs/parsers.pyx", line 695, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: File b'${prefix}/lisa_meta.xls' does not exist

I see that under lisa/demo there are xmlfiles premade ( such as lisa_results_meta_table_human_with_gene_sets.xls ) . I tried to point this file in prefix, and also created an empty lisa_meta.xls file, none of them worked.

I would appreciate the help, thanks!

qinqian commented 4 years ago

Hi Kaltinel, It seems that your configuration was not updated. Could you try the following commands:

wget --user=lisa --password='xxx' http://lisa.cistrome.org/cistromedb_data/lisa_v1.0_hg38.tar.gz tar xvfz lisa_v1.0_hg38.tar.gz lisa_update_conf --folder hg38/ --species hg38

The lisa_meta.xls is located in the hg38/ path. Those lisa_results_meta_table_human_with_gene_sets.xls are the benchmark expression profiles we used in the paper. You can use the demo/AR.symbol to test the installation first.

kaltinel commented 4 years ago

Thank you very much for your reply- I am installing the new files.

Will I need to specify the prefix to the /hg38/ (as a path of lisa_meta.xls) ?

qinqian commented 4 years ago

Yes, please use the absolute path to /hg38/, the lisa_update_conf script will automatically fill in all the configuration information for you.