Running HiCool without internet connection

[malonzm1]

Hi, Do you happen to have a version of HiCool that can run without internet connection? Or can you suggest how I can run HiCool without internet connection (our server has no internet connection for security reasons)?

Br,

[js2264]

You could try and provide a local hg38 fasta file to HiCool(...., genome = 'path/to/hg38.fa'). This will skip downloading of pre-compiled hg38 reference

[malonzm1]

Thanks. What about the conda requirements? Sent from Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: Jacques Serizay ***@***.***> Sent: Tuesday, March 18, 2025 4:47:42 PM To: js2264/HiCool ***@***.***> Cc: Malonzo Maia ***@***.***>; Author ***@***.***> Subject: Re: [js2264/HiCool] Running HiCool without internet connection (Issue #6) You could try and provide a local hg38 fasta file to HiCool(...., genome = 'path/to/hg38.fa'). This will skip downloading of pre-compiled hg38 reference — Reply to this email directly, view it on GitHub<#6 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHXYMJPZKAY5OGAWW4S5FF32VA5Z5AVCNFSM6AAAAABZHJS43GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZTG42TKNJZGM>. You are receiving this because you authored the thread.Message ID: ***@***.***> [js2264]js2264 left a comment (js2264/HiCool#6)<#6 (comment)> You could try and provide a local hg38 fasta file to HiCool(...., genome = 'path/to/hg38.fa'). This will skip downloading of pre-compiled hg38 reference — Reply to this email directly, view it on GitHub<#6 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHXYMJPZKAY5OGAWW4S5FF32VA5Z5AVCNFSM6AAAAABZHJS43GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZTG42TKNJZGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[js2264]

You could perform once the HiCool() function on your submitting node (which I would guess has internet access?), and abort the function once the conda env. is set up. If this is not an option, then you won't be able to use {HiCool}. In that case, I can recommend you hicstuff (which is the main underlying python package used by HiCool). Based on your log, the hicstuff command would look like:

hicstuff pipeline --enzyme DpnII --binning 10000 --duplicates --filter --distance-law --plot --threads 8 --genome hg38.fa MCL_817_22791_GTTTCG_read1_all.fastq.gz MCL_817_22791_GTTTCG_read2_all.fastq.gz