Code

Make picopili portable#56

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Merged

rkwalters merged 49 commits intodevNealelab/picopili:devfrom portableNealelab/picopili:portableCopy head branch name to clipboardMar 20, 2017

+3,127-4,139

Commits

Commits on Sep 28, 2016

• first version of portable blueprint

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  e4b6b1c

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• remove old blueprint, move perl to config, port Utils.pm

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  ab30a12

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Commits on Sep 29, 2016

• separate and simplify config, move imp_prep logs

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  8638404

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• migrate to using picopili.conf file

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  576e70f

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• added picopili configs w defaults, make email optional

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  de4f9d6

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Commits on Sep 30, 2016

• offer separate plague and buigue reference files

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  36d046e

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Commits on Oct 1, 2016

• start integrating blueprint.py, add threading and flexibility

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  6f64c1f

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Commits on Oct 7, 2016

• convert additional tasks to blueprint; minor logging changes

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  e3051bb

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• blueprint remaining direct jobs (not resubs)

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  5df6c38

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• blueprint resubs, using pickled job info

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  ea5e535

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• clean up py imports, add doc with dependencies

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Commits on Oct 8, 2016

• compress multiline commands when parallelizing

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  c996ca8

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• list dependencies; first draft lisa config

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  3d46a80

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• cluster hold, working directory configs

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  04bc27c

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• test of job number hold conditions

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  fe1088c

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• allow job number holds; adjust long job walltimes

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  4f03885

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• add R to lisa environ for primus

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  991b096

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Commits on Oct 12, 2016

• remove refs to unused files; improve ref downloads; avoid implicating Stephan for my .pl changes; misc bugfixes

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  1e2ce65

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• obfuscate email

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  0d25cb5

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Commits on Oct 13, 2016

• add admixture projection option

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• arguments for admix projection vs exemplars

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  e0512bf

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• admix logging and bugfix; blueprint big_mem option

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  2e9b3c1

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• more platform agnostic impute reference args; adjust impute logging

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  c433f15

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Commits on Oct 21, 2016

• admix logging; pass relatedness to reap as kinship

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  a0c6d3e

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Commits on Oct 25, 2016

• fix curly braces in job templates

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  c38c77f

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Commits on Nov 10, 2016

• bugfix args formatting in bg send_job

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  e2567de

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• bugfix arg format, adjust agg mem request in gwas_rel

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  807f20f

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• more detailed logging of missing/broken chunks in gwas agg

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  6361099

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• dont expect .eval output from pca fastmode

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  a9d7734

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Commits on Nov 29, 2016

• ensure allele frequency reported for intended allele

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  0a254d7

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Commits on Dec 5, 2016

• fix specifying reference files with directory, imp_prep cluster

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  f72a891

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• fix directory for shapeit ref info

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  c59be8b

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Commits on Dec 6, 2016

• remove unused refs to hmloc

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  e97bc58

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• fix broken test_exec calls

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  5ee5edf

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Commits on Dec 14, 2016

• more imputation job arg/templating fixes

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  1ba6dd9

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• fix resub of array jobs with 1 task remaining

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  92173c0

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Commits on Mar 1, 2017

• force numeric freqs

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  d34f451

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• improve file checks from args

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  af81898

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• update default loc for admixture on Broad

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  e4f2f26

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• prevent duplicating find/test execs

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  9e57709

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Commits on Mar 2, 2017

• fix admixture plotting without exemplars

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  060f44d

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Commits on Mar 3, 2017

• improve log of plotting cmds

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  81714f8

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• fix mark for unplotted region

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  f6b2bb0

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Commits on Mar 15, 2017

• fix typo

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  bc97a03

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• fix depends broken by Broad Anaconda (mostly for R plots)

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  e937bde

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• adaptive mem reqs for imp agg

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  e5dc9fc

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• add option of arbitrary weights for filter ped

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  3114d17

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• Merge branch 'portable' of https://github.com/Nealelab/picopili into portable

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  5adc766

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• log filter_ped warnings

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