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dockers for single R packages#66

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wkusmirek wants to merge 114 commits intoZSI-Bio:masterZSI-Bio/CNV-opt:masterfrom wkusmirek:r-packages-separeted-in-dockerswkusmirek/CNV-opt:r-packages-separeted-in-dockersCopy head branch name to clipboard

+1,775-885

Commits

Commits on Mar 19, 2018

• dockers for single R packages - init

  wkusmirek

  committed
  ea559a7

• building docker images before running tests - only for speed up dev process

  wkusmirek

  committed
  723d222

• bugfix in Jenkinsfile

  wkusmirek

  committed
  357e36c

• build.sh file without pushing dockers images

  wkusmirek

  committed
  7cd7620

• pushing images in build.sh file

  wkusmirek

  committed
  f72a2ba

• rename docker images

  wkusmirek

  committed
  5de7eff

Commits on Mar 20, 2018

• draft of docker containers for CODEX, Canoes and Exomedepth

  wkusmirek

  committed
  a0cc870

• CANOES package

  wkusmirek

  committed
  be88e85

• CANOES package in Jenkinsfile

  wkusmirek

  committed
  0edbf36

• bugfix

  wkusmirek

  committed
  28e60cd

• Canoes added to docker container

  wkusmirek

  committed
  f3bb5c9

Commits on Mar 22, 2018

• TARGET.QC package in docker

  wkusmirek

  committed
  7a92540

• switch off R tests to speed up development

  wkusmirek

  committed
  28c3311

• TARGET.QC package with reading and writing coverage table

  wkusmirek

  committed
  e515fef

• bugfixes in TARGET.QC package

  wkusmirek

  committed
  905ed26

• building dockers without cache - to reload R packages while development

  wkusmirek

  committed
  53dcff6

• proper order of column in TARGET.QC results

  wkusmirek

  committed
  40292ef

• bugfix

  wkusmirek

  committed
  3a7951d

Commits on Mar 23, 2018

• dockerfile for REFERENCE.SAMPLE.SET.SELECTOR

  wkusmirek

  committed
  1e5f202

• new interface to run_REFERENCE.SAMPLE.SET.SELECTOR method

  wkusmirek

  committed
  86022de

• change arguments order in run_REFERENCE.SAMPLE.SET.SELECTOR function

  wkusmirek

  committed
  da94fbd

• draft of DAG for CODEX cnv caller

  wkusmirek

  committed
  c75ff28

• EXOMEDEPTH package in docker

  wkusmirek

  committed
  3e88016

Commits on Mar 24, 2018

• Dockerfile for EXOMEDEPTHCOV package

  wkusmirek

  committed
  91c7e3c

Commits on Mar 26, 2018

• first version of CODEXCOV package in docker image

  wkusmirek

  committed
  862aabe

• finished dag for ExomeDepth, draft od dag for CANOES

  wkusmirek

  committed
  626f23a

• draft of CANOESCOV with new interface

  wkusmirek

  committed
  7a7beef

• bugfix

  wkusmirek

  committed
  14b1967

• finished dag file for CODEX cnv caller

  wkusmirek

  committed
  02e0c01

• IRanges in docker for CANOESCOV package

  wkusmirek

  committed
  066be68

• add getgc function to CANOESCOV package

  wkusmirek

  committed
  f9f4ffd

• missing libraries in getgc function

  wkusmirek

  committed
  d510815

• bugfixes

  wkusmirek

  committed
  43cec0b

• missing libraries

  wkusmirek

  committed
  f0a6ea0

• libraries in another place

  wkusmirek

  committed
  43997d9

Commits on Mar 27, 2018

• remove libraries from run_CANOESCOV function

  wkusmirek

  committed
  68507f0

• CODEX in CANOESCOV package (only for tests)

  wkusmirek

  committed
  6e6cc47

• tests for building CANOESCOV docker with CODEX dependencies

  wkusmirek

  committed
  1b82b56

• missing CANOES library

  wkusmirek

  committed
  7555622

• bugfix in CANOESCOV libraries

  wkusmirek

  committed
  381555c

Commits on Mar 30, 2018

• first version of new interface to TARGET.QC package

  wkusmirek

  committed
  6e4c1cc

• first version of new interface to REFERENCE.SAMPLE.SET.SELECTOR package

  wkusmirek

  committed
  9a7c043

• test of forcing rebuilding specified docker

  wkusmirek

  committed
  b069d27

• proper name of packege

  wkusmirek

  committed
  7999948

• another test of forcing docker rebuilding

  wkusmirek

  committed
  bc168e9

• another test of rebuilding docker image

  wkusmirek

  committed
  200a8f6

• force to rebuild cnv-opt-reference-sample-set-selector docker

  wkusmirek

  committed
  d3dd140

• bugfix

  wkusmirek

  committed
  b3d1bc9

• bugfix one more time

  wkusmirek

  committed
  2247ef3

• propoer indices

  wkusmirek

  committed
  961e8b3

• bugfix in saveing qc_bed to file

  wkusmirek

  committed
  3da288a

• progress in selecting reference sample set

  wkusmirek

  committed
  54415b6

• firsst version of new interface for exomedepthcov package

  wkusmirek

  committed
  ef805c7

• some clean up in EXOMEDEPTHCOV package

  wkusmirek

  committed
  bd4c87a

• first version new interface to CODEXCOV package

  wkusmirek

  committed
  bb2b86d

• first version of new interface to CANOESCOV package

  wkusmirek

  committed
  100b6f1

• force to rebuild CANOESCOV package

  wkusmirek

  committed
  b7ff805

• bugfix

  wkusmirek

  committed
  f6c966f

• forcing rebuilding only specified dockers - to speed up dev process

  wkusmirek

  committed
  e4b6f80

• coverage table as matrix

  wkusmirek

  committed
  7c0447f

• code clean up

  wkusmirek

  committed
  820a751

Commits on Apr 1, 2018

• bugfix

  wkusmirek

  committed
  f2646ea

• force to reload CODEXCOV package

  wkusmirek

  committed
  f89d041

• dags for codex, canoes and exomedept callers

  wkusmirek

  committed
  7b9c82d

Commits on Apr 6, 2018

• init version of EXOMECOPYCOV package

  wkusmirek

  committed
  ab5bd6d

• bugfix in Dockerfile

  wkusmirek

  committed
  d7c1a6a

Commits on Apr 7, 2018

• bugfix in exomeCopy version

  wkusmirek

  committed
  63f76e7

• force to reload EXOMECOPYCOV package

  wkusmirek

  committed
  ae2061e

• bugfix in forcing reloading package

  wkusmirek

  committed
  f21852f

• bugfix in sampname type

  wkusmirek

  committed
  5933e4e

• missing libraries

  wkusmirek

  committed
  9acf200

• exomeCopy in 1.22 version

  wkusmirek

  committed
  e2f5d9a

• missing libraries

  wkusmirek

  committed
  1412d07

Commits on Apr 8, 2018

• writing detected CNVs to output file

  wkusmirek

  committed
  0e8fa23

Commits on Apr 30, 2018

• random method of selecting reference sample set

  wkusmirek

  committed
  c446c1f

• reload package for selecting reference sample set

  wkusmirek

  committed
  45e10ba

• bugfix

  wkusmirek

  committed
  2856a8d

• bugfix

  wkusmirek

  committed
  2989118

• select reference set based on CANOES method with cov threshold

  wkusmirek

  committed
  7bb4e4b

• bugfix

  wkusmirek

  committed
  c54d436

Commits on May 16, 2018

• investigated reference sample set in EXOMECOPYCOV package (first version)

  wkusmirek

  committed
  7ed767f

• reload package

  wkusmirek

  committed
  43ead0d

• manual forcing package reload

  wkusmirek

  committed
  ca70a81

• DBI package greater or equal to 0.8

  wkusmirek

  committed
  4071094

• force to reload package

  wkusmirek

  committed
  6bcb7f7

• bugfix

  wkusmirek

  committed
  fc5fbd2

• reload package in docker container

  wkusmirek

  committed
  0662e41

• bugfix

  wkusmirek

  committed
  bf7ac7c

• reload package

  wkusmirek

  committed
  6c771b4

• bugfix one more time

  wkusmirek

  committed
  0b0d37a

• merging results

  wkusmirek

  committed
  a88e5db

• clean up Dockerfile

  wkusmirek

  committed
  5d62b84

Commits on May 21, 2018

• kmeans in reference sample set selector - first version

  wkusmirek

  committed
  53f94dc

• force to reload Docker image

  wkusmirek

  committed
  5878140

• bugfix

  wkusmirek

  committed
  ef8dace

• speed up kmeans

  wkusmirek

  committed
  ab4c0e1

• bugfix

  wkusmirek

  committed
  769805a

• changes in order to find a bug

  wkusmirek

  committed
  57b9604

• bugfix

  wkusmirek

  committed
  85c550e

• changes in order to detect bug

  wkusmirek

  committed
  bc2a002

• code clean up, bugfix

  wkusmirek

  committed
  e408aea

Commits on Oct 11, 2018

• CNV.SIMULATOR package init

  wkusmirek

  committed
  a7b6352

• CNV.SIMULATOR package

  wkusmirek

  committed
  6dfcaa8

• first, not tested version of simulating CNVs by downsampling

  wkusmirek

  committed
  918bee2

Commits on Oct 16, 2018

• comment out testing Scala code

  wkusmirek

  committed
  4497545

• comment out everything connected to Scala from Jenkinsfile

  wkusmirek

  committed
  b89bb5f

• bugfix

  wkusmirek

  committed
  c7cc004

• remove unresolved dependencies

  wkusmirek

  committed
  1ed18d2

• force to rebuild cnv-simulator docker

  wkusmirek

  committed
  2f8d051

• printing generated CNVs

  wkusmirek

  committed
  81533bc

• downsample method finished

  wkusmirek

  committed
  a99d5a3

Commits on Oct 17, 2018

• first version of X replacement from Ximmer tool

  wkusmirek

  committed
  0497387

• random male sample changed to the most correlated male sample

  wkusmirek

  committed
  f927dea

Commits on Oct 24, 2018

• force to rebuild docker image

  wkusmirek

  committed
  426bced