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iqbal-lab-org / clockwork

CRyPTIC data processing pipelines
MIT License
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API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit #91

Closed lily616 closed 2 years ago

lily616 commented 2 years ago

Hello, I have a question about running the clockwork, could you give me a suggestion?

The code as the following,

Singularity> nextflow run nextflow/variant_call.nf --ref_dir /tmp/singularity-3.8.0/refrence/ --reads_in1 /tmp/singularity-3.8.0/diyData/1.L350_BDMS190036238-1a_1.fq.clean.gz --reads_in2 /tmp/singularity-3.8.0/diyData/1.L350_BDMS190036238-1a_2.fq.clean.gz --output_dir result --sample_name sample N E X T F L O W ~ version 21.10.0 Pulling nextflow-io/nextflow ... API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit

I have confused me some time, I would grateful for you if you can help me, thank you.

martinghunt commented 2 years ago

You need to have nextflow installed, independently of the singularity container, so that nextflow is in your $PATH. ie running just the command nextflow works. Then run:

nextflow run nextflow/variant_call.nf \
    -with-singularity clockwork_container.img 
    ... etc

where you'll have to replace clockwork_container.img with the name that you used when making the container when running singularity build. And the full command as in the wiki page https://github.com/iqbal-lab-org/clockwork/wiki/Pipelines-without-a-database