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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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version 1.3.r3 #129

Closed jluebeck closed 1 year ago

jluebeck commented 1 year ago

Hi Viraj,

I hope you are doing well! The Mosek team graciously opened a pull request to add support for Mosek 8, 9 and 10+. I have tested their updates and found no differences in output between 1.3.r2 Mosek 8 and the newly updated 1.3.r3 Mosek 8. Mosek 9 does lead to some very small CN estimate changes < 0.02, typically, when compared to Mosek 8, but this is of course negligible. I have also updated the docker and installation instructions for these changes. Users can now install Mosek via pip install, saving them from installing Mosek 8 manually.

The readme also gives instructions for using the cloud-hosted GenePatternNotebook version of AmpliconArchitect, which is just 1.3.r2 with a web interface running on AWS (funded by a grant Vineet has). This means there is no installation required to use that version.

Please let me know if you have any questions! Jens

virajbdeshpande commented 1 year ago

Hi Jens, thanks for adding these updates. Is this PR ready for review and merging?

jluebeck commented 1 year ago

Hi Viraj,

Thanks - yes it is ready for review and merging!

Jens

jluebeck commented 1 year ago

Hi Viraj,

Just an FYI that there is a new version on my branch 1.3.r4. I think this is reflected in the current pull request commit list.

Thanks, Jens

jluebeck commented 1 year ago

Hi Viraj, I resolved the merge conflicts. When you are able, would you be able to review and approve the PR?

Thank you! Jens

jluebeck commented 1 year ago

Hi Viraj, thanks for reviewing the PR. I hope the responses above resolve any remaining questions, and please let me know what you would like to do about the location of the AA docker image.

Thanks, Jens

jluebeck commented 1 year ago

Hi Viraj - are you able to do the merge of this approved PR?

Btw - the AA license is now also registered in the Conda package license info for AmpliconSuite (as well as in the top level of the github repo). Licensing info will also be on the GenePattern interface page in the next day or so.

The .out files are also back, with "-" instead of ":" in the filenames (tested and found no issues).

Thanks, Jens