MIKE Pipeline Command-Line Arguments

Documentation of command-line arguments.

Note: objects in CAPS are fields the user must supply.

mikedb -d DATADIR [options...]

-d DATADIR	directory of data
-gz	option for gzipped fits files

Directory with fits files.
```
mikedb -d /data1/example/directory
```
Directory with gzipped fits files.
```
mikedb -d /data1/example/directory -gz
```

mikesetup -db DATABASE TARGET(S) [options...]

mikesetup -db DATABASE -all [options...]

-all	generates pipelines for all targets
-blue	option generates pipelines for blue frames
-db DATABASE	database file
-flatblue FLATBLUE	location to a specific flatblue frame
-flatkey FLATSTRING	string to search for flat frames in database file
-flatred FLATRED	location to a specific flatred frame
-fringe FRINGE	location to a specific fringe frame
-fringekey FRINGESTRING	string to search for fringe frames in database file
-individual	separate extractions
-lampblue LAMPBLUE	location to a specific lampblue frame
-lampkey LAMPSTRING	string to search for lamp frames in database file
-lampred LAMPRED	location to a specific lampred frame
-logb	option bins extracted spectra logarithmically in wavelength
-mk MAKEFILE	creates a makefile for multiple targets
-noslitfn	option skips the generation and usage of a slit function
-orderkey ORDERSTRING	string to search for order frames in database file
-red	option generates pipelines for red frames
-slitblue SLITBLUE	location to a specific slitblue frame
-slitred SLITRED	location to a specific slitred frame

Mikesetup generating pipeline for ngc3201-e1.
```
mikesetup -db directory.db ngc3201-e1 -red
```
Mikesetup generating pipelines for all red targets in the database directory.
```
mikesetup -db directory.db -red -all
```
Mikesetup generating pipelines for all red and blue targets in the database directory.
```
mikesetup -db directory.db -red -blue -all
```
Mikesetup generating pipelines for all red and blue targets in the database directory and creating a Makefile.
```
mikesetup -db directory.db -red -blue -all -mk Makefile
```

Mikesetup generating pipelines for specific flatkey, orderkey, fringekey and lampkey.

mikesetup -db directory.db -flatkey quartzflatw_milky -orderkey quartzflatw_omilky 
-fringekey dome -lampkey thar -red -blue -all

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