setupForMoirai: setupForMoirai

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Exports environment variables to find Moirai files.

Usage

setupForMoirai(LIBRARY, MOIRAI_USER, MOIRAI_PROJECT, MOIRAI_STAMP = "latest",
  GENOME = c("hg19", "hg38"))

Arguments

LIBRARY	A name identifying a library given in Moirai.
MOIRAI_USER	A Moirai user name (part of the file path).
MOIRAI_PROJECT	A Moirai project name (part of the file path). Note that some Moirai project names look like user names and vice versa.
MOIRAI_STAMP	A Moirai time stamp.
GENOME	A genome identifier, to get default annoation and gene definition.

Details

LOCAL FUNCTION WITH A LOT OF HARDOCODING. If no timestamp is given, it will look for the latest processing.

Using LIBRARY, MOIRAI_USER and MOIRAI_PROJECT, setupForMoirai will find the directory containing the last Moirai run for that library, and export its path in the environment variable PROCESSED_DATA.

It will also set the environment variables GROUP_SHARED, GENE_SYMBOLS and ANNOTATION, to default values.

Value

Prints shell commands that, would have the same effect. This is useful when cut-pasting from knitR workflows that use R to change the environment and then run some shell chunks.

Returns PROCESSED_DATA.

See Also

exportInEnv

Examples

## PROCESSED_DATA <- setupForMoirai(
##   LIBRARY        = '140609_M00528_0024_000000000-A8CBW',
##   MOIRAI_USER    = 'nano-fluidigm',
##   MOIRAI_PROJECT = 'C1_CAGE' )

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.