Add SMNCopyNumberCaller to bioconda and nf-core.

[peterpru]

I would like to use this program as a recipe in bioconda, and as a nf-core module in nextflow.

I am currently adding these, and will update when it is complete.

[freconfarmer]

I am currently trying to learn how to use Anaconda and this program. I have 3 cram files I want it to analyze. I've got as far as all requirements to run, but now trying to create a text file with the right information to run the program.

[peterpru]

I am currently trying to learn how to use Anaconda and this program. I have 3 cram files I want it to analyze. I've got as far as all requirements to run, but now trying to create a text file with the right information to run the program.

Hi @freconfarmer, what do you mean? The input manifest.txt is a list of bam or cram files, where each row is a bam file. Is that your issue? Example below:
In manifest.txt:
/path/to/file.cram
/path/to/file2.cram

I am not the author of this program, so if you have specific issues, I recommend making a new issue or contacting the authors directly.

[peterpru]

Please find SMNcopynumbercaller on bioconda now:
https://anaconda.org/bioconda/smncopynumbercaller

[freconfarmer]

Thanks for your reply. I’m a jack of all trades master of a very few things, not a programmer, and over my head in understanding code🤔 but I’m learning. I was using a win based anaconda, but realized I needed to install pysam-win which smncopynumbercaller won’t recognize, then switched over to Linux and another learning curve. You adding this to bioconda is awesome, I just need to figure out how to install everything on Linux. But I’m a nubie at this.

…

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On Dec 2, 2022, at 7:26 AM, Peter Pruisscher ***@***.***> wrote:  Please find SMNcopynumbercaller on bioconda now: https://anaconda.org/bioconda/smncopynumbercaller — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[xiao-chen-xc]

Thanks so much for making this happen @peterpru !

[peterpru]

Thanks so much for making this happen @peterpru !

No worries @xiao-chen-xc 😄

Thanks for your reply. I’m a jack of all trades master of a very few things, not a programmer, and over my head in understanding code🤔 but I’m learning. I was using a win based anaconda, but realized I needed to install pysam-win which smncopynumbercaller won’t recognize, then switched over to Linux and another learning curve. You adding this to bioconda is awesome, I just need to figure out how to install everything on Linux. But I’m a nubie at this.

No problems @freconfarmer , we all start somewhere, in a while you'll be an expert. For installing smncopynumbercaller to linux, you can install/set-up bioconda https://bioconda.github.io/index.html, and then do conda install smncopynumbercaller, and smncopynumber and its dependencies should then be installed.

[peterpru]

Bioconda:

• https://bioconda.github.io/recipes/smncopynumbercaller/README.html#package-smncopynumbercaller
• conda install smncopynumbercaller

Singularity/docker containers:

• quay.io/biocontainers/smncopynumbercaller:1.1.2--py310h7cba7a3_0
• https://depot.galaxyproject.org/singularity/smncopynumbercaller:1.1.2--py310h7cba7a3_0

nf-core:

• https://nf-co.re/modules
• Installation command: nf-core modules install smncopynumbercaller

All done, closing issue.