Questions tagged [bioconda]

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0 answers
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Aligning PacBio HiFi reads to reference genome using pbmm2

I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am ...
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1 vote
2 answers
65 views

Bioconductor Conda release delay

How long does it take for the latest Bioconductor to end up on Conda? I think I saw a blog post about the challenges with this process, but I cannot find it. For example, Bioconductor 3.13 was ...
  • 2,139
2 votes
1 answer
96 views

Get Dockerfile of a bioconda package

Bioconda packages have associated containers images. E.g. bioconductor-csaw has the image quay.io/biocontainers/bioconductor-csaw...
  • 323
1 vote
1 answer
239 views

How to Installing & Using RDP Classifier through bioconda?

I am interested in using RDP classifier and RDPTools at the command line. In following the docs from RDP, I ran into this issue during the build, after running make...
0 votes
1 answer
175 views

UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux

I have installed some ucsc tools on my Mac computer and it worked fine: Installation ...
  • 2,439
3 votes
1 answer
142 views

Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?

I searched for the package 'snakemake' on my SLURM cluster using: conda search --channel bioconda snakemake and I get many versions, up to 5.4.2. I then try to ...
  • 2,439
8 votes
3 answers
2k views

Getting the licenses of all conda installed packages

I would like to get a list of the licenses of all packages I installed using Conda. pip has what I need in the form of pip-licenses, is there a similar thing for conda?
  • 521
9 votes
3 answers
4k views

Running Snakemake in one single conda env

I have been experimenting a lot lately with Snakemake, I love it. Recently I also switched to using conda (--use-conda) in the way that is advertised. However, I have some issues with it, mostly ...
  • 521
1 vote
3 answers
714 views

How can I install bioconductor-gviz and use it in jupyter notebook?

I tried to install gviz in a conda environment, but that library seems to be incompatible to python and r. I tried to setup a clean environment using ...
  • 1,273
6 votes
1 answer
3k views

Can't install newest Blast from Conda

I have run into an odd situation, where Anaconda repo page clearly states that the newest version of Blast in Bioconda channel is 2.7.1, however the version Conda wants to install (command ...
  • 263
3 votes
1 answer
328 views

Difference between genometools installed with anaconda vs apt-get?

I installed genometools with anaconda conda install -c bioconda genometools. Something is installed though apparently no binary called ...
  • 1,273
1 vote
1 answer
1k views

How to uninstall hmmpress from my conda environment?

I have installed hmmpress on my Mac OS X. It is here: which hmmpress /Users/user/anaconda/bin/hmmpress It is available in my ...
  • 2,439