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chapmanb/cloudbiolinux

cloubiolinux.org website is hijacked or domain expired

The domain registration for cloudbiolinux.org likely expired, and has now been parked by an unrelated entity.

• M-Try
·
• Opened 
  on May 15, 2024
·
• #415

chapmanb/cloudbiolinux

Please submit cloudbiolinux/BCBIO related issues to bcbio github

https://github.com/bcbio/bcbio-nextgen/issues

• naumenko-sa
·
• Opened 
  on Nov 14, 2021
·
• #392

chapmanb/cloudbiolinux

Installation problem conda package libtiff

Installing via bcbio results in error package libtiff-4.3.0-hf544144_1 requires libdeflate =1.7, 1.8.0a0, but none of the providers can be installed . Presumably it is related to this recent commit? DISTRIB_ID=Ubuntu ...

• rchekaluk
·
• 1
·
• Opened 
  on Oct 24, 2021
·
• #386

chapmanb/cloudbiolinux

Incorrect Ensembl release version for hg38 transcripts.yaml

The 92 Ensembl release number of hg38 transcripts.yaml is currently incorrect. It was built against Ensembl 94, which is noted in the YAML comments. I just double checked the reference against Ensembl ...

• mjsteinbaugh
·
• Opened 
  on Oct 1, 2021
·
• #385

chapmanb/cloudbiolinux

Don't use both mamba and conda to install packages

The issue lies in https://github.com/chapmanb/cloudbiolinux/blob/924029a5614bfb730ae8e980b0b879a87cf42ba8/cloudbio/package/conda.py#L67 and https://github.com/chapmanb/cloudbiolinux/blob/924029a5614bfb730ae8e980b0b879a87cf42ba8/cloudbio/package/conda.py#L71 ...

• lbeltrame
·
• Opened 
  on Dec 14, 2020
·
• #374

chapmanb/cloudbiolinux

tar -p option causes quota issues in case quota are enforced on group level

I m encountering issues installing the bcbio pipeline on a HPC infrastructure where quota are strictly enforced on the group level AND file system location level. all files in (for example) /projects/mygroup ...

• vdejager
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• 3
·
• Opened 
  on Mar 20, 2020
·
• #349

chapmanb/cloudbiolinux

limit conda environments

Hi, I was wondering if it d be possible to put an effort together to limit the conda evironments currently installed buy cloudbiolinux. I suppose the following steps are pretty easy targets - bump ...

• matthdsm
·
• 1
·
• Opened 
  on Feb 24, 2020
·
• #340

chapmanb/cloudbiolinux

Integrate additional GiaB samples for validation

It would be great to also include NA24694 and NA24695 of the genome in a bottle samples to the standard bcbio installation. Or is there a reason why this may be not feasible?

• sam-ber
·
• 1
·
• Opened 
  on Feb 12, 2020
·
• #334

chapmanb/cloudbiolinux

Broad FTP login error is causing bcbio-nextgen data upgrade to fail

See related issue filed over at bcbio-nextgen: https://github.com/bcbio/bcbio-nextgen/issues/3021 Looks like the gsapubftp login might need to be updated? Here s the relevant code: https://github.com/chapmanb/cloudbiolinux/search?q=gsapubftp ...

• mjsteinbaugh
·
• 7
·
• Opened 
  on Nov 22, 2019
·
• #329

chapmanb/cloudbiolinux

Problems with centralized conda installation

I have a problem with this section: https://github.com/chapmanb/cloudbiolinux/blob/3d60fde49ebcfdc6d8dac37a44573de06e64433d/cloudbio/package/conda.py#L208-L237 The background is that I wanted to install ...

• karl616
·
• 2
·
• Opened 
  on Oct 4, 2019
·
• #324

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