Comments (10)
Hi, I was wondering if you have a timeline for making a release. The package recipe is almost finished (https://github.com/bcbio/bioconda-recipes/tree/scramble-recipe/recipes/scramble) and we are ready to submit it to Bioconda as soon as a GitHub release of Scramble is published. It doesn't have to be polished (using the current latest commit on master is fine) since it is fairly easy to update the package when new versions come out. We are looking forward to making Scramble easier to install and use.
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@hackdna sorry I missed that before. here you go: https://github.com/GeneDx/scramble/releases/tag/v1.0.1
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Thanks for your help. Conda package v1.0.1 has been published: https://anaconda.org/bioconda/scramble
Some badges to add to README.md
: https://anaconda.org/bioconda/scramble/badges
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Yes, it is okay to make a bioconda package for scramble (and would be much appreciated), but I'm afraid we can't budge on the license. We're also in the process of updating scramble to have clipped read deletion calling and to output VCFs, so if you wait a few weeks, those features should be available.
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Hi Rebecca,
Great! I'll get on making the package. No worries about budging on the license, just thought I'd ask.
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Hi Rebecca, Bioconda does not allow downloading the source code directly from a VCS for building packages (https://bioconda.github.io/contributor/linting.html#policy). Would you mind creating a release?
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Thanks +1 to what Ilya said-- we can make the package but we need a release version to make it against. It is nice because once we do it that way, bioconda will pick up all subsequent releases you all make automatically so you'll always have an up to date version in bioconda.
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Hi @hackdna and @roryk, thanks so much for the interest and the help getting scramble into bioconda. We will make a release and let you know.
from scramble.
@hackdna @roryk here you go: https://github.com/GeneDx/scramble/releases/tag/v1.0.0
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@mfinelli Thanks very much! Could you create a release v1.0.1 to match the cluster_identifier version (#10)?
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Related Issues (20)
- Row names warning message HOT 1
- VCF Creation Issue HOT 3
- Segmentation fault HOT 1
- What to evaluate should be a mandatory argument HOT 1
- Error in write.table HOT 1
- filtering calls
- negative length vectors are not allowed HOT 3
- VCF not valid HOT 1
- Error in writing vcd
- Rare clusters have all "n"s in 4th field, causing R to fail
- Getting "Segmentation fault (core dumped)" when running against some bam files. HOT 1
- SCRAMble.R have error report.
- Empty vcf file after Error: subscript contains invalid names; result.txt_MEIs.txt shows MEI calls HOT 1
- Feature request: Add option for reference to cluster_identifier HOT 2
- Update scramble to 1.0.2 in bioconda HOT 2
- Fail to write VCF file - negative coordinates HOT 3
- Error in .Call2("XStringSet_align_pairwiseAlignment", pattern, subject, : key 0 not in lookup table HOT 4
- Help with call filtering HOT 7
- Help with MEI annotation HOT 5
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