Devon Ryan
Devon Ryan
There's an unusual edge case where recipes have both a run_test.sh and tests. The run_test.sh is used by conda-build but the tests in the meta.yaml are used during mulled testing....
I'd like to include this in one of our pipelines, can you tag a release for SalmonTools? I'll add it to Bioconda then :)
Nothing other than alphanumeric (only ascii letters), - and _ are allowed in sample names by Illumina and we should really enforce that in Parkour, since otherwise we always run...
It would be quite nice if users received a warning if they specify completely stupid names for their samples. A stupid name would be any of the following: 1. A...
Annoyingly, having a last name like `O'Meara` will break Illumina's software, since it results in project names like `92_O'Meara_Boehm` in the sample sheet. I've editted that instance in the database,...
We have a [HiC-related tool](https://github.com/maxplanck-ie/HiCExplorer) that's [available in Galaxy](https://toolshed.g2.bx.psu.edu/repository/browse_repositories?sort=name&operation=view_or_manage_repository&f-free-text-search=hicexplorer&id=f1554978eeb3da8b) that requires SAM/BAM input that is not coordinate sorted. As input, we normally use BAM files produced by bwa mem, which...
While rebuilding portcullis in Bioconda under python 3.10, I noticed the python version is incorrectly parsed in the configure script: ```configure: Found python version: 3.10.5 2022-08-02T14:01:19.5433788Z 14:01:19 BIOCONDA INFO (OUT)...
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During the most recent migration (this was intended to migrate htslib, but ended up migrating perl to 5.32.1 as well) the following couldn't be built under OSX: (dependencies of each...
Suppose we have the following entries in a vcf file: ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FOO chr2 12345 123 AC A . PASS DP=699;MQ=250.00;FractionInformativeReads=0.953;SoftClipRatio=0.03;ANN=A|frameshift_variant|HIGH|ENSG|ENSG|transcript|ENSTA|protein_coding|5/10|c.3267delC|p.Phe1090fs|3339/4233|3267/4089|1089/1362||INFO_REALIGN_3_PRIME,A|intron_variant|MODIFIER|ENSG|ENSG|transcript|ENSTB|protein_coding|3/3|c.*124+4493delG|||||| GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB...