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Recent Releases of containers

containers - Comorment-Containers-v1.9.1 (COSGAP)

What's Changed

  • Update pullallcontainers.py by @espenhgn in https://github.com/comorment/containers/pull/299
  • test bump old scikit-learn, sksurv versions by @espenhgn in https://github.com/comorment/containers/pull/300
  • seaborn 0.12.1->0.13.2; pandas 1.5.0->2.2.3 by @espenhgn in https://github.com/comorment/containers/pull/301
  • python3.sif: containerize tools by @espenhgn in https://github.com/comorment/containers/pull/303

Full Changelog: https://github.com/comorment/containers/compare/v1.9.0...v1.9.1

- R
Published by espenhgn 11 months ago

containers - Comorment-Containers-v1.9.0 (COSGAP)

This is a major update with a number of changes since 1.8.1 (see below). Notably, the project is referred to as COSGAP (COntainerized Statistical Genetics Analysis Pipelines) as described in our paper, and container builds are now removed from the git history and are available from ghcr.io as described in the installation procedures.

What's Changed

  • Revised autodocs build by @espenhgn in https://github.com/comorment/containers/pull/231
  • Updated LDpred2 examples by @deepchocolate in https://github.com/comorment/containers/pull/233
  • Deprecate Saige by @ttfiliz in https://github.com/comorment/containers/pull/239
  • Documentation updates by @espenhgn in https://github.com/comorment/containers/pull/240
  • references by @espenhgn in https://github.com/comorment/containers/pull/242
  • citation stuff by @espenhgn in https://github.com/comorment/containers/pull/243
  • add --extract and --exclude options to filter snps in gwas.py by @ttfiliz in https://github.com/comorment/containers/pull/244
  • r.sif: Rstudio-server docs by @espenhgn in https://github.com/comorment/containers/pull/248
  • gwas.sif: build regenie with HAS_BOOST_IOSTREAM=1 by @espenhgn in https://github.com/comorment/containers/pull/250
  • Build container image hello:latest using build action by @espenhgn in https://github.com/comorment/containers/pull/252
  • Revert "Build container image hello:latest using build action " by @espenhgn in https://github.com/comorment/containers/pull/253
  • Update runldpred2slurm.job by @espenhgn in https://github.com/comorment/containers/pull/254
  • add support for additional options in gwas.py by @ttfiliz in https://github.com/comorment/containers/pull/246
  • Add container build/push actions by @espenhgn in https://github.com/comorment/containers/pull/260
  • Fixed wrong Docker build target by @espenhgn in https://github.com/comorment/containers/pull/262
  • search and replace r fix by @espenhgn in https://github.com/comorment/containers/pull/264
  • Update gSEM Git SHA by @juuf in https://github.com/comorment/containers/pull/265
  • bump wget version by @espenhgn in https://github.com/comorment/containers/pull/266
  • fix GLIBCXX_3.4.30 not found; conda env; fix broken tests by @espenhgn in https://github.com/comorment/containers/pull/268
  • buggered ldak download by @espenhgn in https://github.com/comorment/containers/pull/272
  • python3: add missing packages by @espenhgn in https://github.com/comorment/containers/pull/274
  • Run unit tests during Docker build procedure by @espenhgn in https://github.com/comorment/containers/pull/277
  • Fix broken build-push action by @espenhgn in https://github.com/comorment/containers/pull/279
  • Missing tools/packages to Python3/R containers by @espenhgn in https://github.com/comorment/containers/pull/281
  • bump fossil version by @espenhgn in https://github.com/comorment/containers/pull/282
  • Containerize missing tools/update by @espenhgn in https://github.com/comorment/containers/pull/289
  • Build-push actions fail: oras: not found by @espenhgn in https://github.com/comorment/containers/pull/291
  • LDpred2: Add --file-drop-snps argument by @espenhgn in https://github.com/comorment/containers/pull/293
  • Containerize tools by @espenhgn in https://github.com/comorment/containers/pull/295
  • structure for singularity/containers directory by @espenhgn in https://github.com/comorment/containers/pull/296
  • updated changelog for 1.9.0 by @espenhgn in https://github.com/comorment/containers/pull/298

New Contributors

  • @juuf made their first contribution in https://github.com/comorment/containers/pull/265

Full Changelog: https://github.com/comorment/containers/compare/v1.8.1...v1.9.0

- R
Published by espenhgn about 1 year ago

containers - Comorment-Containers-v1.8.1

This is 1st bugfix release of the CoMorMent-Containers project since v1.8.0 release. Confer also the CHANGELOG for an overview of changes since the v1.8.0 release

What's Changed

  • Minor changes to documentation + suggestion of TOC by @ofrei in https://github.com/comorment/containers/pull/228
  • gwas.py: fixed gwas demo run and IID column position by @ttfiliz in https://github.com/comorment/containers/pull/234

Full Changelog: https://github.com/comorment/containers/compare/v1.8.0...v1.8.1

- R
Published by espenhgn almost 2 years ago

containers - CoMorMent-Containers-v1.8.0

This is 1st feature release of the CoMorMent-Containers project since v1.7.1 release. Confer also the CHANGELOG for an overview of changes since the v1.6.1 release

What's Changed

  • r.sif: Add CC-GWAS R package by @espenhgn in https://github.com/comorment/containers/pull/226
  • calculateLD.R: Fixed incorrect SNP map by @deepchocolate in https://github.com/comorment/containers/pull/178

Full Changelog: https://github.com/comorment/containers/compare/v1.7.1...v1.8.0

- R
Published by espenhgn almost 2 years ago

containers - CoMorMent-Containers-v1.7.1

Comorment-Containers-v1.7.1 Latest

This is 1st bugfix release of the CoMorMent-Containers project since v1.7.0 release. Confer also the CHANGELOG for an overview of changes since the v1.7.0 release

What's Changed

  • ldpred2.R: fix hg_38 should be hg38 and hg_18 should be hg18 by @espenhgn in https://github.com/comorment/containers/pull/224

Full Changelog: https://github.com/comorment/containers/compare/v1.7.0...v1.7.1

- R
Published by espenhgn about 2 years ago

containers - Comorment-Containers-v1.7.0

This is 1st feature release of the CoMorMent-Containers project since v1.6.0 release. Confer also the CHANGELOG for an overview of changes since the v1.6.0 release

What's Changed

  • gwas.sif: Add samtools, bedtools, liftOver, upgrade others by @espenhgn in https://github.com/comorment/containers/pull/222

Full Changelog: https://github.com/comorment/containers/compare/v1.6.0...v1.7.0

- R
Published by espenhgn about 2 years ago

containers - Comorment-Containers-v1.6.0

This is 1st feature release of the CoMorMent-Containers project since v1.5.1 release. Confer also the CHANGELOG for an overview of changes since the v1.5.1 release

What's Changed

  • Add/update requested gwas.sif binaries by @espenhgn in https://github.com/comorment/containers/pull/214

Full Changelog: https://github.com/comorment/containers/compare/v1.5.1...v1.6.0

- R
Published by espenhgn about 2 years ago

containers - Comorment-Containers-v1.5.1

This is 1st bugfix release of the CoMorMent-Containers project since v1.5.0 release. Confer also the CHANGELOG for an overview of changes since the v1.5.0 release

What's Changed

  • Docs builds are failing on readthedocs.io by @espenhgn in https://github.com/comorment/containers/pull/208

Full Changelog: https://github.com/comorment/containers/compare/v1.5.0...v1.5.1

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.5.0

This is 1st feature release of the CoMorMent-Containers project since v1.4.0 release. Confer also the CHANGELOG for an overview of changes since the v1.4.0 release

What's Changed

  • Add PRS tools by @espenhgn in https://github.com/comorment/containers/pull/107

Full Changelog: https://github.com/comorment/containers/compare/v1.4.0...v1.5.0

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.4.0

This is 10th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • Fixed failed installation of minimac4 in gwas.sif by @espenhgn in https://github.com/comorment/containers/pull/196

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.4.0

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.9

This is 9th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • LDpred2.R: redirect temporary data during runs by @espenhgn in https://github.com/comorment/containers/pull/204

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.9

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.8

This is 8th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • LDpred2: Build 37/38 behavior/documentation by @espenhgn in https://github.com/comorment/containers/pull/202

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.8

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.7

This is 7th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • LDpred2/createBackingFile.R: process .bgen files by @espenhgn in https://github.com/comorment/containers/pull/200

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.7

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.6

This is 6th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • LDpred2.R: if --merge-by-rsid is used, ignore --col-bp <arg> by @espenhgn in https://github.com/comorment/containers/pull/193

Full Changelog: https://github.com/comorment/containers/compare/v1.3.5...v1.3.6

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.5

This is 5th bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • Info on ldpred2.R --help functionality by @espenhgn in https://github.com/comorment/containers/pull/192

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.5

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.4

This is 4th bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • Fix #187 by @ofrei in https://github.com/comorment/containers/pull/188

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.4

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.3

This is 3rd bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • Fix LDpred2 error with uppercase chromosome column header by @espenhgn in https://github.com/comorment/containers/pull/180
  • Documentation fixes by @espenhgn in https://github.com/comorment/containers/pull/182
  • LDpred2: Removed counting of missing genotypes by @deepchocolate in https://github.com/comorment/containers/pull/183
  • Fix #174 - sync releases to TSD by @ofrei in https://github.com/comorment/containers/pull/184

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.3

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.2

This is 2nd bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • Fix LDpred2 error with uppercase chromosome column header by @espenhgn in https://github.com/comorment/containers/pull/180
  • Documentation fixes by @espenhgn in https://github.com/comorment/containers/pull/182

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.2

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.1

This is 1st bugfix release of the CoMorMent-Containers project since v1.3.0 release Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

  • Fix LDpred2 error with uppercase chromosome column header by @espenhgn in https://github.com/comorment/containers/pull/180

Full Changelog: https://github.com/comorment/containers/compare/v1.3.0...v1.3.1

- R
Published by espenhgn over 2 years ago

containers - CoMorMent-Containers-v1.3.0

This is the 3rd maintenance/feature release of the CoMorMent-Containers project. Confer also the CHANGELOG for an overview of changes since the v1.2 release

What's Changed

  • LDPred2: Effective sample size, cores used, hyperparameters by @deepchocolate in https://github.com/comorment/containers/pull/173
  • prep 1.3.0 release by @espenhgn in https://github.com/comorment/containers/pull/176

Full Changelog: https://github.com/comorment/containers/compare/v1.2...v1.3.0

- R
Published by espenhgn almost 3 years ago

containers - CoMorMent-Containers-v1.2

CoMorMent-Containers-v1.2

This is the 2nd maintenance/feature release of the CoMorMent-Containers project. Confer also the CHANGELOG for an overview of changes since the v1.1 release

What's Changed

  • LDpred2 fixes by @deepchocolate in https://github.com/comorment/containers/pull/94
  • LDpred2.R uses external ld matrix (partial fix for #108) by @ofrei in https://github.com/comorment/containers/pull/109
  • add citation.cff and badges by @espenhgn in https://github.com/comorment/containers/pull/113
  • set appropriate number of CPU cores by @espenhgn in https://github.com/comorment/containers/pull/115
  • Remove reference to ldsc.sif (moved) by @espenhgn in https://github.com/comorment/containers/pull/114
  • QQ plots w. confidence bands by @ttfiliz in https://github.com/comorment/containers/pull/118
  • unit tests for gwas.py by @ttfiliz in https://github.com/comorment/containers/pull/119
  • --variance-standardize for columns without variation by @ttfiliz in https://github.com/comorment/containers/pull/121
  • Deepchocolate/ldpred2 updates fixes by @espenhgn in https://github.com/comorment/containers/pull/122
  • Allow custom name for IID columns by @ofrei in https://github.com/comorment/containers/pull/123
  • update config for flake8 linter by @espenhgn in https://github.com/comorment/containers/pull/126
  • Reformat gwas.py and combine_figures.py by @ofrei in https://github.com/comorment/containers/pull/128
  • removed redundant --sumstats-sep arg by @espenhgn in https://github.com/comorment/containers/pull/129
  • LD-estimation for LDpred2 using bigSNPR by @deepchocolate in https://github.com/comorment/containers/pull/117
  • change home to temporary folder in testgwasking by @ttfiliz in https://github.com/comorment/containers/pull/136
  • Change repo for R packages in r.sif by @espenhgn in https://github.com/comorment/containers/pull/132
  • some minor fixes to LDpred2 imputation by @espenhgn in https://github.com/comorment/containers/pull/139
  • LDpred2 imputation by @deepchocolate in https://github.com/comorment/containers/pull/131
  • removed redundant LDpred2 example by @espenhgn in https://github.com/comorment/containers/pull/141
  • Remove --file-pheno, --col-pheno and --col-pheno-from-fam args in ldpred2.R scripts by @espenhgn in https://github.com/comorment/containers/pull/142
  • LDpred2: Testing produced scores against tutorial results by @deepchocolate in https://github.com/comorment/containers/pull/146
  • Sumstats: Add column and position by @deepchocolate in https://github.com/comorment/containers/pull/143
  • LDpred2: Append score to existing output file by @deepchocolate in https://github.com/comorment/containers/pull/150
  • fixed print statements by @espenhgn in https://github.com/comorment/containers/pull/156
  • Make complementSumstats.R write file output by default by @espenhgn in https://github.com/comorment/containers/pull/159
  • clarify --geno-file-rds arg by @espenhgn in https://github.com/comorment/containers/pull/161
  • fixed bad parsing of args by @espenhgn in https://github.com/comorment/containers/pull/164
  • bumped version to reflect current state by @espenhgn in https://github.com/comorment/containers/pull/166
  • Restructured file and folder layout by @espenhgn in https://github.com/comorment/containers/pull/167
  • Add RELEASES.md file by @espenhgn in https://github.com/comorment/containers/pull/170
  • Prep release v1.2 by @espenhgn in https://github.com/comorment/containers/pull/172

New Contributors

  • @ttfiliz made their first contribution in https://github.com/comorment/containers/pull/118

Full Changelog: https://github.com/comorment/containers/compare/v1.1...v1.2

- R
Published by espenhgn almost 3 years ago

containers - CoMorMent-Containers-v1.1

CoMorMent-Containers-v1.1

This is the first maintenance/feature release of the CoMorMent-Containers project. Confer also the CHANGELOG for an overview of changes since the initial v1.0.0 release

What's Changed

  • Fixes incorrect --vcfField format by @rzetterberg in https://github.com/comorment/containers/pull/24
  • Resolves #34 by @rzetterberg in https://github.com/comorment/containers/pull/35
  • Split out mixer by @ofrei in https://github.com/comorment/containers/pull/53
  • Add issue/PR templates by @espenhgn in https://github.com/comorment/containers/pull/48
  • migrating files from GH/comorment/gwas@47a23f0 by @espenhgn in https://github.com/comorment/containers/pull/51
  • Remove libquadmath0 from builds by @espenhgn in https://github.com/comorment/containers/pull/60
  • Use Mambaforge for python3.sif builds by @espenhgn in https://github.com/comorment/containers/pull/63
  • Revise Minimac4/bgenix installation in gwas.sif by @espenhgn in https://github.com/comorment/containers/pull/64
  • Bump base image to Ubuntu:20.04 by @espenhgn in https://github.com/comorment/containers/pull/65
  • Pin software versions by @espenhgn in https://github.com/comorment/containers/pull/66
  • Basic test suite by @espenhgn in https://github.com/comorment/containers/pull/67
  • Add Shapeit4 (and dependency HTSlib) to gwas.sif by @espenhgn in https://github.com/comorment/containers/pull/71
  • GH actions (docker&python lint, greetings, stale) by @espenhgn in https://github.com/comorment/containers/pull/72
  • add FaST-LMM v0.6.3 to python3.sif by @ofrei in https://github.com/comorment/containers/pull/74
  • Remove broken links to MiXeR usage scenarios by @ofrei in https://github.com/comorment/containers/pull/82
  • Add tests for metal, qctool ingwas.sif. by @espenhgn in https://github.com/comorment/containers/pull/84
  • LD score regression moved to separate github repo by @ofrei in https://github.com/comorment/containers/pull/86
  • Strip container builds of source files etc. by @espenhgn in https://github.com/comorment/containers/pull/79
  • Remove ldsc.sif file by @ofrei in https://github.com/comorment/containers/pull/87
  • clean up install of htslib, bcftools, shapeit4 by @espenhgn in https://github.com/comorment/containers/pull/89
  • r.sif: add R bigsnpr and related tools for LDpred2 analysis by @espenhgn in https://github.com/comorment/containers/pull/91
  • Add autogeneration of documentation using Sphinx by @espenhgn in https://github.com/comorment/containers/pull/88
  • updated changelog for future v1.1 by @espenhgn in https://github.com/comorment/containers/pull/97
  • Split out matlab by @ofrei in https://github.com/comorment/containers/pull/98
  • Move MAGMA, LAVA, ldblock to comorment/magma repo by @ofrei in https://github.com/comorment/containers/pull/100
  • Move out enigma-cnv.sif , ipsychcnv.sif, tryggve_query.sif by @ofrei in https://github.com/comorment/containers/pull/101
  • some changelog/readme updates for v1.1 by @espenhgn in https://github.com/comorment/containers/pull/99

New Contributors

  • @ofrei made their first contribution in https://github.com/comorment/containers/pull/53

Full Changelog: https://github.com/comorment/containers/compare/v1.0.0...v1.1

- R
Published by espenhgn about 3 years ago

containers - CoMorMent-Containers-v1.0.0

initial release 70502c11d662218181ac79a846a0937a enigma-cnv.sif 1ddd2831fcab99371a0ff61a8b2b0970 gwas.sif b02fe60c087ea83aaf1b5f8c14e71bdf hello.sif 1ab5d82cf9d03ee770b4539bda44a5ba ipsychcnv.sif 6d024aed591d8612e1cc628f97d889cc ldsc.sif 2e638d1acb584b42c6bab569676a92f8 matlabruntime.sif 331688fb4fb386aadaee90f443b50f8c python3.sif cdbfbddc9e5827ad9ef2ad8d346e6b82 r.sif b8c1727227dc07e3006c0c8070f4e22e regenie.sif 97f75a45a39f0a2b3d728f0b8e85a401 regenie3.sif 20e01618bfb4b0825ef8246c5a63aec5 saige.sif 5de579f750fb5633753bfda549822a32 tryggve_query.sif

What's Changed

  • Makes gwas.py an executable by @rzetterberg in https://github.com/comorment/containers/pull/4
  • Fixes broken link to sumstats_specification.md by @rzetterberg in https://github.com/comorment/containers/pull/3
  • Update meta_simu.md by @johnshorter in https://github.com/comorment/containers/pull/18

New Contributors

  • @johnshorter made their first contribution in https://github.com/comorment/containers/pull/18

Full Changelog: https://github.com/comorment/containers/commits/v1.0.0

- R
Published by ofrei over 4 years ago