Tag: LZMA

bioconductor – Trouble installing Rhtslib in R/R studio

I’m using RStudio on Ubuntu 18 and I’m trying to install the htslib package from the Bioconductor repo, but I’m stuck now. This is what I get: * installing *source* package ‘Rhtslib’ … ** using non-staged installation via StagedInstall field ** libs cd “htslib-1.7” && make -f “/usr/lib/R/etc/Makeconf” -f “Makefile.Rhtslib”…

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Running samtools view on bam affects the number of variants called by both haplotypecaller and deepvariant – C samtools

Thanks for getting back to me Valeriu. As you suggested, I used the latest commit from the develop branch in my pipeline, and the results look good. I was able to replicate the numbers from samtools v1.10.2 and v1.11 for both variant callers. FYI $ docker run scilifelabram/htslib:dev_proper /opt/samtools/samtools version…

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install GenomicFeatures fail

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

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The Biostar Herald for Tuesday, August 17, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by lakhujanivijay,…

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