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Make portable version the master version #57

Merged
merged 52 commits into from
Mar 20, 2017
Merged

Make portable version the master version #57

merged 52 commits into from
Mar 20, 2017

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rkwalters
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Merging portable version to master. See full description in #56.

@rkwalters
add column w sex to pca output (easier covar)
dc16f8e
@rkwalters
first version of portable blueprint
e4b6b1c
@rkwalters
remove old blueprint, move perl to config, port Utils.pm
ab30a12
@rkwalters
separate and simplify config, move imp_prep logs
8638404
@rkwalters
migrate to using picopili.conf file
576e70f
@rkwalters
added picopili configs w defaults, make email optional
de4f9d6
@rkwalters
offer separate plague and buigue reference files
36d046e
@rkwalters
start integrating blueprint.py, add threading and flexibility
6f64c1f
@rkwalters
convert additional tasks to blueprint; minor logging changes
e3051bb
@rkwalters
blueprint remaining direct jobs (not resubs)
5df6c38
@rkwalters
blueprint resubs, using pickled job info
ea5e535
@rkwalters
clean up py imports, add doc with dependencies
f313cee
@rkwalters
compress multiline commands when parallelizing
c996ca8
@rkwalters
list dependencies; first draft lisa config
3d46a80
@rkwalters
cluster hold, working directory configs
04bc27c
@rkwalters
test of job number hold conditions
fe1088c
@rkwalters
allow job number holds; adjust long job walltimes
4f03885
@rkwalters
add R to lisa environ for primus
991b096
@rkwalters
remove refs to unused files; improve ref downloads; avoid implicating…
1e2ce65 
… Stephan for my .pl changes; misc bugfixes
@rkwalters
obfuscate email
0d25cb5
@rkwalters
add admixture projection option
44df0df
@rkwalters
arguments for admix projection vs exemplars
e0512bf
@rkwalters
admix logging and bugfix; blueprint big_mem option
2e9b3c1
@rkwalters
more platform agnostic impute reference args; adjust impute logging
c433f15
@rkwalters
Merge pull request #55 from Nealelab/pca_sex
eebef48 
add column w sex to pca output (easier covar)
@rkwalters
admix logging; pass relatedness to reap as kinship
a0c6d3e
@rkwalters
fix curly braces in job templates
c38c77f
@rkwalters
bugfix args formatting in bg send_job
e2567de
@rkwalters
bugfix arg format, adjust agg mem request in gwas_rel
807f20f
@rkwalters
more detailed logging of missing/broken chunks in gwas agg
6361099
@rkwalters
dont expect .eval output from pca fastmode
a9d7734
@rkwalters
ensure allele frequency reported for intended allele
0a254d7
@rkwalters
fix specifying reference files with directory, imp_prep cluster
f72a891
@rkwalters
fix directory for shapeit ref info
c59be8b
@rkwalters
remove unused refs to hmloc
e97bc58
@rkwalters
fix broken test_exec calls
5ee5edf
@rkwalters
more imputation job arg/templating fixes
1ba6dd9
@rkwalters
fix resub of array jobs with 1 task remaining
92173c0
@rkwalters
force numeric freqs
d34f451
@rkwalters
improve file checks from args
af81898
@rkwalters
update default loc for admixture on Broad
e4f2f26
@rkwalters
prevent duplicating find/test execs
9e57709
@rkwalters
fix admixture plotting without exemplars
060f44d
@rkwalters
improve log of plotting cmds
81714f8
@rkwalters
fix mark for unplotted region
f6b2bb0
@rkwalters
fix typo
bc97a03
@rkwalters
fix depends broken by Broad Anaconda (mostly for R plots)
e937bde
@rkwalters
adaptive mem reqs for imp agg
e5dc9fc
@rkwalters
add option of arbitrary weights for filter ped
3114d17
@rkwalters
Merge branch 'portable' of https://github.com/Nealelab/picopili into …
5adc766 
…portable
@rkwalters
log filter_ped warnings
16cbf54
@rkwalters
Merge pull request #56 from Nealelab/portable
39f35f4 
Make picopili portable
@rkwalters rkwalters merged commit 525c573 into master Mar 20, 2017
@rkwalters rkwalters mentioned this pull request Apr 3, 2017
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@rkwalters