startmitcr: Start MiTCR directly from the package.

Description Usage Arguments Details Examples

Description

Start the MiTCR tools directly from the package with given settings.

Usage

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startmitcr(.input = "", .output = "", ..., .file.path = "",
  .mitcr.path = "~/programs/", .mem = "4g")

Arguments

.input, .output

Input and output files.

...

Specify input and output files and arguments of the MITCR without first '-' to run it.

.file.path

Path prepending to .input and .output. If input and output is empty, but .file.path is specified, than process all files from the folder .file.path

.mitcr.path

Path to MiTCR .jar file.

.mem

Volume of memory available to MiTCR.

Details

Don't use spaces in paths! You should have insalled JDK 1.7 to make it works.

Examples

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## Not run: 
# Equal to
# java -Xmx8g -jar ~/programs/mitcr.jar -pset flex 
#      -level 2 ~/data/raw/TwA1_B.fastq.gz ~/data/mitcr/TwA1_B.txt
startmitcr('raw/TwA1_B.fastq.gz', 'mitcr/TwA1_B.txt', .file.path = '~/data/',
  pset = 'flex', level = 1, 'debug', .mitcr.path = '~/programs/', .mem = '8g')

## End(Not run)


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