New susie method #151
New susie method #151
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| sudo R -e "install.packages('tidyr', repos='http://cran.rstudio.com/')" | ||
| sudo R -e "install.packages('base', repos='http://cran.rstudio.com/')" | ||
| sudo R -e "install.packages('stats', repos='http://cran.rstudio.com/')" | ||
| # sudo R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/coloc/coloc_5.1.0.tar.gz', repos = NULL, type = 'source')" |
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Clean up, remove unneeded lines
| sudo yum install -y python3-devel | ||
| sudo yum install -y R | ||
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| # Install R-4.1.0 |
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Remove all of these commented bits
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| # install yum dependencies | ||
| sudo yum install -y python3-devel | ||
| sudo yum install -y R |
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Do you need to install R? I thought it was installed by default on the boxes.
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No longer needed to install R. The current version is good now.
susie/built.sbt
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| val Versions = new { | |||
| val Aggregator = "0.3.4-SNAPSHOT" | |||
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Change this to 3.5 which I just released
susie/project/build.properties
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| sbt.version=1.5.0 | |||
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change this to 1.8.2 which more up to date computers will only have
| parser.add_option("","--phenotype", default=None) | ||
| parser.add_option("","--ancestry", default=None) | ||
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| (options, args) = parser.parse_args() |
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just args = parser.parse_args() and use args instead of options
| subprocess.run('cat input/*.json > input.json', shell=True) | ||
| shutil.rmtree('input') | ||
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| def make_ld_files(directory): |
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| package org.broadinstitute.dig.aggregator.methods.susie | |||
susie/src/main/scala/MakeSuSiE.scala
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| class MakeSuSiE(implicit context: Context) extends Stage { | ||
| import MemorySize.Implicits._ | ||
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| val ancestrySpecific: Input.Source = Input.Source.Success("out/metaanalysis/bottom-line/ancestry-clumped/*/*/") |
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For now I guess we'll just mess with EU data since you only have EU data right. Replace the second '*' with ancestry=EU and that should make it specific
susie/src/main/scala/MakeSuSiE.scala
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| import MemorySize.Implicits._ | ||
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| val ancestrySpecific: Input.Source = Input.Source.Success("out/metaanalysis/bottom-line/ancestry-clumped/*/*/") | ||
| // val mixedDatasets: Input.Source = Input.Source.Success("variants/*/*/*/") |
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remove this, this will never be used
susie/src/main/scala/MakeSuSiE.scala
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| /** Map inputs to their outputs. */ | ||
| override val rules: PartialFunction[Input, Outputs] = { | ||
| case ancestrySpecific(phenotype, ancestry) => Outputs.Named(s"$phenotype/${ancestry.split('=').last}") |
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if you are going to specify ancestry=EU above this has to be changed since there is only one wildcard now:
case ancestrySpecific(phenotype) => Outputs.Named(s"$phenotype/EU")
will do it
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