Comments (1)
List of what we will include:
- hello.sif
- gwas.sif
- python3.sif
- r.sif
- saige.sif
Omissions:
- ldsc.sif; mixer, ldsc, magma, pleiofdr (cf. #40).
- enigma-cnv.sif and matlabruntime.sif (cf. #55).
- LAVA/lava_partitioning (#54)
- shapeit2, impute4 (LICENSE issues, #50)
- bgenix, htslib (cf. Alex)
Adds rudimentary test suite for built containers which can be run locally using pytest (py.test -v tests
; cf #57)
from containers.
Related Issues (20)
- LDpred2: Test LDSC regression result HOT 1
- LDpred2: complementSumstats.R: `sumstats` -> `fileSumstats`
- `LDpred2/complementSumstats.R`: rename `#CHROM` column in output HOT 2
- Versioned release planning/schedule
- `complementSumstats.R`: More arguments than defaults for `--columns-append` throws error HOT 2
- `gwas.py gwas` crashes with a `KeyError: 0` trying to rename the IID column HOT 5
- version/version.py version info is wrong
- Document steps needed to make a new release of this repository HOT 1
- Fixed broken links in online documentation
- Make release `Containers-v1.2` HOT 1
- Document syncing to TSD/p697 in RELEASES.md HOT 1
- LDpred2: `--out-merge` does not produce diagnostic plots correctly
- `LDpred2`: Error when using LD-data produced by `calculatedLD.R` HOT 6
- `LDpred2`: Error when filtering characters in chromosome column HOT 4
- `LDpred2`: Remove time thief HOT 1
- regenie in gwas.sif should be updated
- Regression in gwas.py in handling of info, maf, hwe and geno filters
- LDpred2: Build 37/38 behavior/documentation HOT 2
- LDpred2 doc suggestions.
- LDpred2.R: if `--merge-by-rsid` option is used, ignore `--col-bp` arg HOT 2
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