Closed MPvdBurg closed 6 years ago
Hi Thijs,
Have you tried installing rad_haplotyper using conda (see the instructions in the README)? That should help with the dependency issues.
Chris
Hi Chris,
Yes I did, but that didn't work for me so I tried the older(?) way.
I used
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
Then
$ conda install rad_haplotyper
Gives me
PackageNotFoundError: Packages missing in current channels:
- rad_haplotyper
We have searched for the packages in the following channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.continuum.io/pkgs/main/osx-64
- https://repo.continuum.io/pkgs/main/noarch
- https://repo.continuum.io/pkgs/free/osx-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/osx-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/osx-64
- https://repo.continuum.io/pkgs/pro/noarch
Same holds for
$ conda install -c bioconda rad_haplotyper
and
conda create -n rad_haplotyper_env rad_haplotyper
Best, Thijs
Hi Thijs,
Right now, the bioconda install is limited to Linux and not OS X. Sorry.
Jon
-- Jon Puritz
On November 27, 2017 at 16:40:03, ThijsvandenBurg (notifications@github.com) wrote:
Hi Chris,
Yes I did, but that didn't work for me so I tried the older(?) way.
I used
conda config --add channels r conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda
Then $ conda install rad_haplotyper Gives me
PackageNotFoundError: Packages missing in current channels:
- rad_haplotyper
We have searched for the packages in the following channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.continuum.io/pkgs/main/osx-64
- https://repo.continuum.io/pkgs/main/noarch
- https://repo.continuum.io/pkgs/free/osx-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/osx-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/osx-64
- https://repo.continuum.io/pkgs/pro/noarch
Same holds for $ conda install -c bioconda rad_haplotyper and conda create -n rad_haplotyper_env rad_haplotyper
Best, Thijs
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I don't recognize the error, but maybe there are multiple versions of the Vcf.pm module in the path? If you install a fresh version of vcftools with conda or brew, do you get the same error?
conda create -n vcftools_env vcftools
source activate vcftools_env
vcftools --version
Hi Chris,
$ vcftools --version
VCFtools (0.1.15)
Still gives the same error, yes.
Were you able to check if you have two Vcf.pm modules in the path?
There were no additional in my path except the one in /Library/Perl/5.18/Vcf.pm which it keeps redefining. Just to be sure I removed the ones on my laptop, still same result.
Did you download Vcf.pm manually or did you use the one that installs with vcftools?
Hi,
Let me first say I'm a programming roocky, although I'm learning :) I am having an issue with setting up my laptop (Mac) to run the rad_haplotyper script. I downloaded all Perl modules but when I run the script in the 'snp filtering' tutorial I get this message:
When I check whether I have the Vcf module, this returns:
So it seems I do have the module, but it doesn't work. I was wondering whether people have similar issues with the Vcf module on Mac?
Thanks in advance, Thijs