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Make picopili portable #56

Merged
merged 49 commits into from
Mar 20, 2017
Merged

Make picopili portable #56

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e4b6b1c
first version of portable blueprint
rkwalters Sep 28, 2016
ab30a12
remove old blueprint, move perl to config, port Utils.pm
rkwalters Sep 28, 2016
8638404
separate and simplify config, move imp_prep logs
rkwalters Sep 29, 2016
576e70f
migrate to using picopili.conf file
rkwalters Sep 29, 2016
de4f9d6
added picopili configs w defaults, make email optional
rkwalters Sep 29, 2016
36d046e
offer separate plague and buigue reference files
rkwalters Sep 30, 2016
6f64c1f
start integrating blueprint.py, add threading and flexibility
rkwalters Oct 1, 2016
e3051bb
convert additional tasks to blueprint; minor logging changes
rkwalters Oct 7, 2016
5df6c38
blueprint remaining direct jobs (not resubs)
rkwalters Oct 7, 2016
ea5e535
blueprint resubs, using pickled job info
rkwalters Oct 7, 2016
f313cee
clean up py imports, add doc with dependencies
rkwalters Oct 7, 2016
c996ca8
compress multiline commands when parallelizing
rkwalters Oct 8, 2016
3d46a80
list dependencies; first draft lisa config
rkwalters Oct 8, 2016
04bc27c
cluster hold, working directory configs
rkwalters Oct 8, 2016
fe1088c
test of job number hold conditions
rkwalters Oct 8, 2016
4f03885
allow job number holds; adjust long job walltimes
rkwalters Oct 8, 2016
991b096
add R to lisa environ for primus
rkwalters Oct 8, 2016
1e2ce65
remove refs to unused files; improve ref downloads; avoid implicating…
rkwalters Oct 12, 2016
0d25cb5
obfuscate email
rkwalters Oct 12, 2016
44df0df
add admixture projection option
rkwalters Oct 13, 2016
e0512bf
arguments for admix projection vs exemplars
rkwalters Oct 13, 2016
2e9b3c1
admix logging and bugfix; blueprint big_mem option
rkwalters Oct 13, 2016
c433f15
more platform agnostic impute reference args; adjust impute logging
rkwalters Oct 13, 2016
a0c6d3e
admix logging; pass relatedness to reap as kinship
rkwalters Oct 21, 2016
c38c77f
fix curly braces in job templates
rkwalters Oct 25, 2016
e2567de
bugfix args formatting in bg send_job
rkwalters Nov 10, 2016
807f20f
bugfix arg format, adjust agg mem request in gwas_rel
rkwalters Nov 10, 2016
6361099
more detailed logging of missing/broken chunks in gwas agg
rkwalters Nov 10, 2016
a9d7734
dont expect .eval output from pca fastmode
rkwalters Nov 10, 2016
0a254d7
ensure allele frequency reported for intended allele
rkwalters Nov 29, 2016
f72a891
fix specifying reference files with directory, imp_prep cluster
rkwalters Dec 5, 2016
c59be8b
fix directory for shapeit ref info
rkwalters Dec 5, 2016
e97bc58
remove unused refs to hmloc
rkwalters Dec 6, 2016
5ee5edf
fix broken test_exec calls
rkwalters Dec 6, 2016
1ba6dd9
more imputation job arg/templating fixes
rkwalters Dec 14, 2016
92173c0
fix resub of array jobs with 1 task remaining
rkwalters Dec 14, 2016
d34f451
force numeric freqs
rkwalters Mar 1, 2017
af81898
improve file checks from args
rkwalters Mar 1, 2017
e4f2f26
update default loc for admixture on Broad
rkwalters Mar 1, 2017
9e57709
prevent duplicating find/test execs
rkwalters Mar 1, 2017
060f44d
fix admixture plotting without exemplars
rkwalters Mar 2, 2017
81714f8
improve log of plotting cmds
rkwalters Mar 3, 2017
f6b2bb0
fix mark for unplotted region
rkwalters Mar 3, 2017
bc97a03
fix typo
rkwalters Mar 15, 2017
e937bde
fix depends broken by Broad Anaconda (mostly for R plots)
rkwalters Mar 15, 2017
e5dc9fc
adaptive mem reqs for imp agg
rkwalters Mar 15, 2017
3114d17
add option of arbitrary weights for filter ped
rkwalters Mar 15, 2017
5adc766
Merge branch 'portable' of https://github.com/Nealelab/picopili into …
rkwalters Mar 15, 2017
16cbf54
log filter_ped warnings
rkwalters Mar 15, 2017
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5 changes: 4 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
bin/py_helpers.pyc
bin/blueprint.pyc
bin/args_pca.pyc
bin/args_ped.pyc
bin/args_qc.pyc
bin/args_gwas.pyc
bin/args_chunks.pyc
bin/args_impute.pyc

bin/test_debug
lib/plague*
lib/buigue*
1 change: 1 addition & 0 deletions CONFIG
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@@ -0,0 +1 @@
./bin/config_pico.pl
1 change: 1 addition & 0 deletions GET_REFS
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./bin/get_refs.sh
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