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freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF

MIT License

140 stars 24 forks source link

No releases #25

Closed pneerincx closed 3 years ago

pneerincx commented 3 years ago

Commit messages contain phrases like new release or new version, but there are no versioned releases/tags for this repo. That makes it hard to create a reproducible deployment for reproducible science...

freeseek commented 3 years ago

@pneerincx yes, it is a bit complicated to make releases due to the strong dependency on HTSlib and BCFtools. I have not decided how to settle that yet. For now you could either use the combination of BCFtools and the latest commit (e.g. 1.10.2-0c4cd07) or you can use the releases from this page.

pneerincx commented 3 years ago

@freeseek I understand the dependency on BCFtools and HTSlib complicates the installation, but that should not stop you from hitting the draft new release button. All you have to do is settle on a version number and you are done. This will give us at least a version for gtc2vcf. If that version mentions in a README, release notes or something similar which version of HTSlib and BCFtools it was tested with that would be a nice bonus, but even without reference to a specific version of those dependencies a versioned release for the gtc2vcf code is welcome!

The "this page" link above gives me:

Not Found
The requested URL /software/gtc2vcf was not found on this server.

freeseek commented 3 years ago

As I said, for now, there are releases on this page: http://software.broadinstitute.org/software/gtc2vcf

pneerincx commented 3 years ago

As I said, for now, there are releases on this page: http://software.broadinstitute.org/software/gtc2vcf

Is that website maybe only accessible from some internal network at the Broad?

http://software.broadinstitute.org is resolvable, but returns a rather empty page containing only the DNS name: software.broadinstitute.org
http://software.broadinstitute.org/software as well as http://software.broadinstitute.org/software/gtc2vcf return:
```
Not Found
The requested URL ... was not found on this server.
```

pneerincx commented 3 years ago

Looks like error is caused by an automatic redirect from http to https. The https version of the URL returns the "Not Found" error. Could be a browser issue. Anyway, the http URL works and I see the BCFtools + HTSlib version is listed there for each gtc2vcf version: thanks!