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dockers for single R packages #66

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ea559a7
dockers for single R packages - init
wkusmirek Mar 19, 2018
723d222
building docker images before running tests - only for speed up dev p…
wkusmirek Mar 19, 2018
357e36c
bugfix in Jenkinsfile
wkusmirek Mar 19, 2018
7cd7620
build.sh file without pushing dockers images
wkusmirek Mar 19, 2018
f72a2ba
pushing images in build.sh file
wkusmirek Mar 19, 2018
5de7eff
rename docker images
wkusmirek Mar 19, 2018
a0cc870
draft of docker containers for CODEX, Canoes and Exomedepth
wkusmirek Mar 20, 2018
be88e85
CANOES package
wkusmirek Mar 20, 2018
0edbf36
CANOES package in Jenkinsfile
wkusmirek Mar 20, 2018
28e60cd
bugfix
wkusmirek Mar 20, 2018
f3bb5c9
Canoes added to docker container
wkusmirek Mar 20, 2018
7a92540
TARGET.QC package in docker
wkusmirek Mar 22, 2018
28c3311
switch off R tests to speed up development
wkusmirek Mar 22, 2018
e515fef
TARGET.QC package with reading and writing coverage table
wkusmirek Mar 22, 2018
905ed26
bugfixes in TARGET.QC package
wkusmirek Mar 22, 2018
53dcff6
building dockers without cache - to reload R packages while development
wkusmirek Mar 22, 2018
40292ef
proper order of column in TARGET.QC results
wkusmirek Mar 22, 2018
3a7951d
bugfix
wkusmirek Mar 22, 2018
1e5f202
dockerfile for REFERENCE.SAMPLE.SET.SELECTOR
wkusmirek Mar 23, 2018
86022de
new interface to run_REFERENCE.SAMPLE.SET.SELECTOR method
wkusmirek Mar 23, 2018
da94fbd
change arguments order in run_REFERENCE.SAMPLE.SET.SELECTOR function
wkusmirek Mar 23, 2018
c75ff28
draft of DAG for CODEX cnv caller
wkusmirek Mar 23, 2018
3e88016
EXOMEDEPTH package in docker
wkusmirek Mar 23, 2018
91c7e3c
Dockerfile for EXOMEDEPTHCOV package
wkusmirek Mar 24, 2018
862aabe
first version of CODEXCOV package in docker image
wkusmirek Mar 26, 2018
626f23a
finished dag for ExomeDepth, draft od dag for CANOES
wkusmirek Mar 26, 2018
7a7beef
draft of CANOESCOV with new interface
wkusmirek Mar 26, 2018
14b1967
bugfix
wkusmirek Mar 26, 2018
02e0c01
finished dag file for CODEX cnv caller
wkusmirek Mar 26, 2018
066be68
IRanges in docker for CANOESCOV package
wkusmirek Mar 26, 2018
f9f4ffd
add getgc function to CANOESCOV package
wkusmirek Mar 26, 2018
d510815
missing libraries in getgc function
wkusmirek Mar 26, 2018
43cec0b
bugfixes
wkusmirek Mar 26, 2018
f0a6ea0
missing libraries
wkusmirek Mar 26, 2018
43997d9
libraries in another place
wkusmirek Mar 26, 2018
68507f0
remove libraries from run_CANOESCOV function
wkusmirek Mar 27, 2018
6e6cc47
CODEX in CANOESCOV package (only for tests)
wkusmirek Mar 27, 2018
1b82b56
tests for building CANOESCOV docker with CODEX dependencies
wkusmirek Mar 27, 2018
7555622
missing CANOES library
wkusmirek Mar 27, 2018
381555c
bugfix in CANOESCOV libraries
wkusmirek Mar 27, 2018
6e4c1cc
first version of new interface to TARGET.QC package
wkusmirek Mar 30, 2018
9a7c043
first version of new interface to REFERENCE.SAMPLE.SET.SELECTOR package
wkusmirek Mar 30, 2018
b069d27
test of forcing rebuilding specified docker
wkusmirek Mar 30, 2018
7999948
proper name of packege
wkusmirek Mar 30, 2018
bc168e9
another test of forcing docker rebuilding
wkusmirek Mar 30, 2018
200a8f6
another test of rebuilding docker image
wkusmirek Mar 30, 2018
d3dd140
force to rebuild cnv-opt-reference-sample-set-selector docker
wkusmirek Mar 30, 2018
b3d1bc9
bugfix
wkusmirek Mar 30, 2018
2247ef3
bugfix one more time
wkusmirek Mar 30, 2018
961e8b3
propoer indices
wkusmirek Mar 30, 2018
3da288a
bugfix in saveing qc_bed to file
wkusmirek Mar 30, 2018
54415b6
progress in selecting reference sample set
wkusmirek Mar 30, 2018
ef805c7
firsst version of new interface for exomedepthcov package
wkusmirek Mar 30, 2018
bd4c87a
some clean up in EXOMEDEPTHCOV package
wkusmirek Mar 30, 2018
bb2b86d
first version new interface to CODEXCOV package
wkusmirek Mar 30, 2018
100b6f1
first version of new interface to CANOESCOV package
wkusmirek Mar 30, 2018
b7ff805
force to rebuild CANOESCOV package
wkusmirek Mar 30, 2018
f6c966f
bugfix
wkusmirek Mar 30, 2018
e4b6f80
forcing rebuilding only specified dockers - to speed up dev process
wkusmirek Mar 30, 2018
7c0447f
coverage table as matrix
wkusmirek Mar 30, 2018
820a751
code clean up
wkusmirek Mar 30, 2018
f2646ea
bugfix
wkusmirek Apr 1, 2018
f89d041
force to reload CODEXCOV package
wkusmirek Apr 1, 2018
7b9c82d
dags for codex, canoes and exomedept callers
wkusmirek Apr 1, 2018
ab5bd6d
init version of EXOMECOPYCOV package
wkusmirek Apr 6, 2018
d7c1a6a
bugfix in Dockerfile
wkusmirek Apr 6, 2018
63f76e7
bugfix in exomeCopy version
wkusmirek Apr 7, 2018
ae2061e
force to reload EXOMECOPYCOV package
wkusmirek Apr 7, 2018
f21852f
bugfix in forcing reloading package
wkusmirek Apr 7, 2018
5933e4e
bugfix in sampname type
wkusmirek Apr 7, 2018
9acf200
missing libraries
wkusmirek Apr 7, 2018
e2f5d9a
exomeCopy in 1.22 version
wkusmirek Apr 7, 2018
1412d07
missing libraries
wkusmirek Apr 7, 2018
0e8fa23
writing detected CNVs to output file
wkusmirek Apr 8, 2018
c446c1f
random method of selecting reference sample set
wkusmirek Apr 30, 2018
45e10ba
reload package for selecting reference sample set
wkusmirek Apr 30, 2018
2856a8d
bugfix
wkusmirek Apr 30, 2018
2989118
bugfix
wkusmirek Apr 30, 2018
7bb4e4b
select reference set based on CANOES method with cov threshold
wkusmirek Apr 30, 2018
c54d436
bugfix
wkusmirek Apr 30, 2018
7ed767f
investigated reference sample set in EXOMECOPYCOV package (first vers…
wkusmirek May 16, 2018
43ead0d
reload package
wkusmirek May 16, 2018
ca70a81
manual forcing package reload
wkusmirek May 16, 2018
4071094
DBI package greater or equal to 0.8
wkusmirek May 16, 2018
6bcb7f7
force to reload package
wkusmirek May 16, 2018
fc5fbd2
bugfix
wkusmirek May 16, 2018
0662e41
reload package in docker container
wkusmirek May 16, 2018
bf7ac7c
bugfix
wkusmirek May 16, 2018
6c771b4
reload package
wkusmirek May 16, 2018
0b0d37a
bugfix one more time
wkusmirek May 16, 2018
a88e5db
merging results
wkusmirek May 16, 2018
5d62b84
clean up Dockerfile
wkusmirek May 16, 2018
53f94dc
kmeans in reference sample set selector - first version
wkusmirek May 21, 2018
5878140
force to reload Docker image
wkusmirek May 21, 2018
ef8dace
bugfix
wkusmirek May 21, 2018
ab4c0e1
speed up kmeans
wkusmirek May 21, 2018
769805a
bugfix
wkusmirek May 21, 2018
57b9604
changes in order to find a bug
wkusmirek May 21, 2018
85c550e
bugfix
wkusmirek May 21, 2018
bc2a002
changes in order to detect bug
wkusmirek May 21, 2018
e408aea
code clean up, bugfix
wkusmirek May 21, 2018
a7b6352
CNV.SIMULATOR package init
wkusmirek Oct 11, 2018
6dfcaa8
CNV.SIMULATOR package
wkusmirek Oct 11, 2018
918bee2
first, not tested version of simulating CNVs by downsampling
wkusmirek Oct 11, 2018
4497545
comment out testing Scala code
wkusmirek Oct 16, 2018
b89bb5f
comment out everything connected to Scala from Jenkinsfile
wkusmirek Oct 16, 2018
c7cc004
bugfix
wkusmirek Oct 16, 2018
1ed18d2
remove unresolved dependencies
wkusmirek Oct 16, 2018
2f8d051
force to rebuild cnv-simulator docker
wkusmirek Oct 16, 2018
81533bc
printing generated CNVs
wkusmirek Oct 16, 2018
a99d5a3
downsample method finished
wkusmirek Oct 16, 2018
0497387
first version of X replacement from Ximmer tool
wkusmirek Oct 17, 2018
f927dea
random male sample changed to the most correlated male sample
wkusmirek Oct 17, 2018
426bced
force to rebuild docker image
wkusmirek Oct 24, 2018
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reload package
wkusmirek committed May 16, 2018
commit 6c771b4264a3de7bd474b0723364558fa4f8e3f2
1 change: 1 addition & 0 deletions Docker/cnv-opt-exomecopycov/Dockerfile
Original file line number Diff line number Diff line change
@@ -4,6 +4,7 @@ MAINTAINER biodatageeks <[email protected]>
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('GenomeInfoDb')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('BSgenome.Hsapiens.UCSC.hg19')"

RUN pwd
RUN pwd
RUN pwd