Release

[micknudsen]

Hi,

I would like to (try to) contribute a bioconda recipe for ctat-genome-lib-builder, but there has never been a release. Have you considered making one?

Thanks,
Michael

[brianjohnhaas]

Hi Michael, I wouldn't bother... the system works fine for our routine builds of certain genomes/annotations, but often requires customization for others. It's not as plug-n-play as one would like.

…

On Tue, May 28, 2024 at 3:16 PM Michael Knudsen ***@***.***> wrote: Hi, I would like to (try to) contribute a bioconda recipe for ctat-genome-lib-builder, but there has never been a release. Have you considered making one? Thanks, Michael — Reply to this email directly, view it on GitHub <#19>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX4YKLQV3MS2JJQVRGLZETJZPAVCNFSM6AAAAABINQZZISVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZDCNZVGI3DOMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[micknudsen]

Thanks! I'm using STAR-Fusion and CTAT-SPLICING in my production workflow where I manage all software using conda. I'm working on a recipe for CTAT-SPLICING, and it would be nice to have one for ctat-genome-lib-builder, too. While it works fine by just running the scripts, it triggers my OCD that I can't have everything in conda 😄

In my previous workflow, I used the plug-n-play references, but now I've invested some energy in harmonizing everything across the entire workflow (tumor-normal DNA and tumor RNA) to make sure that the exact same reference genome and GENCODE annotation are used everywhere. I use a version of hg38 with errors masked, and it works fine with ctat-genome-lib-builder.

[brianjohnhaas]

No one's going to stop you from making bioconda packages. ;-) While I love using it for other stuff, I tend to use singularity or docker for these tools myself.

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On Wed, May 29, 2024 at 12:28 AM Michael Knudsen ***@***.***> wrote: Thanks! I'm using STAR-Fusion and CTAT-SPLICING in my production workflow where I manage all software using conda. I'm working on a recipe for CTAT-SPLICING, and it would be nice to have one for ctat-genome-lib-builder, too. While it works fine by just running the scripts, it triggers my OCD that I can't have everything in conda 😄 In my previous workflow, I used the plug-n-play references, but now I've invested some energy in harmonizing everything across the entire workflow (tumor-normal DNA and tumor RNA) to make sure that the exact same reference genome and GENCODE annotation are used everywhere. I use a version of hg38 with (errors)[https://www.nature.com/articles/s41587-021-01158-1] masked, and it works fine with ctat-genome-lib-builder. — Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3CTXJ445EJ4SGMGGDZEVKO7AVCNFSM6AAAAABINQZZISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZWGQ4TAMJTGM> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>