search

gao-lab / GLUE

Graph-linked unified embedding for single-cell multi-omics data integration
MIT License
347 stars 50 forks source link

Error on scglue.genomics.rna_anchored_guidance_graph #109

Open travilucas opened 6 months ago

travilucas commented 6 months ago

Hello, I have the error when running guidance = scglue.genomics.rna_anchored_guidance_graph(rna, atac) when using the data provided in the tutorial. The error stated "sortBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method. I tried every method you provided in issues. Fortuenly, I figure the error out through adding absolute path to bedtools to system PATH. 

bedtools_path = '/home/data/t220310/miniconda3/envs/py3109/bin/bedtools'
os.environ['PATH'] += os.pathsep + os.path.dirname(bedtools_path)
print(os.environ['PATH'])
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/home/data/t220310/miniconda3/envs/py3109/bin

But a new error occurs,NotImplementedError: "sortBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method. image

Here is my basic environment information. image

I will appreciate if you could help me to figure it out. Thanks!

Yours, Lucas

travilucas commented 6 months ago

Sorry,there was something wrong with my statement at the beginning.The first error is this. image

Jeff1995 commented 5 months ago

Hi @travilucas! Thanks for the report. Did you try solutions in #81? Would that solve your problem?

Khalid-Usman commented 5 months ago

@Jeff1995 @travilucas I am facing the same issue, and the error suggest me to install bedtools using conda install -c bioconda bedtools. I have installed it successfully, still it's showing me the wrong path. 

khalid@server:~$ which bedtools
/home/khalid/anaconda3/envs/GLUE/bin/bedtools
khalid@server:~$ /home/khalid/anaconda3/envs/GLUE/bin/bedtools -version
bedtools v2.27.1

Note: I am not a sudo user at server

Khalid-Usman commented 5 months ago

I have solved it by downloading the static binary file from the link, https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static then, I run the following commands, which bedtools //in response you will get the path

mv bedtools.static.binary path
chmod a+x path