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qmarcou / IGoR

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:
https://qmarcou.github.io/IGoR/
GNU General Public License v3.0
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Chain IGoR commands #51

Closed penuts7644 closed 4 years ago

penuts7644 commented 4 years ago

Hi Quentin,

Is it possible to chain IGoR commands? When I try to run something like this, it seems to work fine...

igor -set_wd $WDPATH -batch foo -read_seqs test.txt -species human -chain beta -align --all -evaluate -output --scenarios 10

or do I have to separate the commands and run them one by one?

Cheers, Wout

qmarcou commented 4 years ago

Hi Wout, Yes I have designed the command line processing such that you can chain all commands as long as it makes sense, if the provided command line chain makes some operation ambiguous an error will arise and Igor will terminate with an error message.