9 votes
Accepted

Can't install newest Blast from Conda

I was able to reproduce your problem, even in a blank environment. ...
James Hawley's user avatar
  • 1,384
7 votes

Difference between genometools installed with anaconda vs apt-get?

These appear to be two separate collections of tools. The conda version is a collection of python scripts whereas the apt version is based on a C library. So, as you might expect, the python version ...
LucasBoatwright's user avatar
7 votes

Getting the licenses of all conda installed packages

To my knowledge there's no single listing of the licenses, but you can: conda list | awk '{if(NR>3) printf("%s=%s", $1, $2)}' | xargs conda info | grep license ...
Devon Ryan's user avatar
  • 19.6k
5 votes

Running Snakemake in one single conda env

A good practice is to provide yml file along with your Snakefile. This file should contain all the enviroment definitions that ...
finswimmer's user avatar
  • 1,342
5 votes
Accepted

Running Snakemake in one single conda env

Using only the --use-conda directive, snakemake copies environments somewhere in the local .snakemake directory. This is ...
Sebastian Müller's user avatar
4 votes

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

# Install the BiocManager package first install.packages("BiocManager") library("BiocManager") # Then install the Gviz package BiocManager::install("Gviz")
Aedin's user avatar
  • 156
3 votes
Accepted

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

Did you try following the installation instructions? Try this in R: source("https://bioconductor.org/biocLite.R") BiocInstaller::biocLite(c("Gviz"))
Jared Andrews's user avatar
3 votes
Accepted

Bioconductor Conda release delay

I started the roll-out on the 30th in the evening. There's not much of a delay for the October Bioconductor release, but for the summer release we first have to build the newest R version and then ...
Devon Ryan's user avatar
  • 19.6k
2 votes

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

I created a file .condarc in my home directory with the following content: channels: - conda-forge - bioconda - defaults and it works now. I don't ...
Biomagician's user avatar
  • 2,459
1 vote

Getting the licenses of all conda installed packages

I can't comment, but here's an improvement for the top answer to list more information: ...
Tom Sproul's user avatar
1 vote

Getting the licenses of all conda installed packages

This one uses JQ for parsing and querying conda generated json output (https://stedolan.github.io/jq/) ...
Luuk Peters's user avatar
1 vote
Accepted

Get Dockerfile of a bioconda package

The Dockerfile is generated by galaxy-utils, so I'm not entirely sure what it looks like. However you should be able to generate such a "mulled" container as documented here. In short, ...
Devon Ryan's user avatar
  • 19.6k
1 vote

How to Installing & Using RDP Classifier through bioconda?

The benefit of using the conda package is that you no longer need to know or care exactly where the jar files are (that many java-based packages require this is TERRIBLE design). The example ...
Devon Ryan's user avatar
  • 19.6k
1 vote

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

Short answer: respect the case of the tool name Longer story below Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed ...
Biomagician's user avatar
  • 2,459
1 vote

Running Snakemake in one single conda env

Inside your Snakefile you can provide the same conda: directive to each rule. If you install your pipeline in a central location and have everyone use the same ...
Devon Ryan's user avatar
  • 19.6k
1 vote

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

Use BiocManager::install() ...
Alex Yahiaoui Martinez's user avatar
1 vote

How to uninstall hmmpress from my conda environment?

This time conda uninstall hmmer in the root environment did the job. The sequence of commands that led me there is shown below. Thanks Devon Ryan. ...
Biomagician's user avatar
  • 2,459

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