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VIGNETTE.txt
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# TRegGA: Getting Started
Makefile_TRegGA-orig is the master makefile to run the complete TRegGA workflow, from
read preparation to de novo assembly and reference-guided assembly. The individual steps
(read preparation; target selection; de novo assembly; reference-guided assembly) can
be executed individually using the master makefile with pertinent targets or by running
appropriately edited makefiles in the respective subdirectories. Using the master
makefile facilitates the process by editing 0Record-* scripts that in turn create and
run subtask makefiles.
The dependency structure of the subtasks is as follows:
reads -> target
| \ |
| \ |
> > >
denovo -> rfguided
The all-in-one excution should work well in standard cases. Fine tuning of parameters
may best be done by editing copies of the subtask makefiles.
The following variables must be set in a copy of Makefile_TRegGA-orig:
CHECKONLY yes [default] or no [means that you actually want to run make]
NUMPROC e.g., 8
CULTIVAR e.g., "DA GANG ZHAN"
SYNONYM e.g., Dagangzhan
TARGET e.g., NbSWEET13
REFERENCE e.g., OsjCHR12
FROM e.g., 17290000
TO e.g., 17320000
From the commandline, the entire workflow could be executed as follows:
make CHECKONLY=yes NUMPROC=8 CULTIVAR='\"DA GANG ZHAN\"' SYNONYM=Dagangzhan TARGET=NbSWEET13 REFERENCE=OsjCHR12 FROM=17290000 TO=17320000 -d -f Makefile_TRegGA-orig >& showme
Because we set CHECKONLY=yes, this command should only print to file "showme" what will be executed.
(Note: CHECKONLY=yes is the default, so you could leave out this argument for the same result.)
The "-d" flag to make is optional. It will show the dependencies.
egrep "remake" showme
will list all the targets that need to be remade.
In detail, what is meant to be executed is the following:
1) In reads:
Create a script file 0Record-Dagangzhan and run the script. This will create a
subdirectory Dagangzhan, put Makefile_GPR_Dagangzhan in that directory, and run it.
2) In targets:
Create a script file 0Record-NbSWEET13 and run the script. This will create
files NBSWEET13.*, needed for the reference-guided assembly.
3) In assembly/denovo:
Create a script file 0Record-Dagangzhan and run the script. This will create a
subdirectory Dagangzhan, put Makefile_denovo_Dagangzhan in that directory, and run it.
4) In assembly/rfguided:
Create a script file 0Record-Dagangzhan-on-NbSWEET13 and run the script. This
will create a subdirectory Dagangzhan-on-NbSWEET13, put
Makefile_RGA_Dagangzhan-on-NbSWEET13 in that directory, and run it.
If all looks ok, then to run make, simply replace the CHECKONLY=yes with CHECKONLY=no (and leave out the -d):
make CHECKONLY=no NUMPROC=8 CULTIVAR='\"DA GANG ZHAN\"' SYNONYM=Dagangzhan TARGET=NbSWEET13 REFERENCE=OsjCHR12 FROM=17290000 TO=17320000 -f Makefile_TRegGA-orig >& err
Notes:
- The CULTIVAR argument must be in quotes (allowing spaces).
- The SYNONYM argument must be a single word (no spaces, special characters allowed).
- The TARGET argument should uniquely identify the target specified by REFERENCE, FROM - TO range.
If you want to change the range later, then use a different label or remove the existing TARGET.*
files in subdirectory targets.
Targets for the subtasks are identified by the following files:
reads ${TRegGA_DIR)/reads/SYNONYM/SYNONYM_1.fa
targets ${TRegGA_DIR}/targets/TARGET.embl
denovo ${TRegGA_DIR}/assembly/denovo/SYNONYM/SYNONYM-GF/SYNONYM-GF.gapfilled.final.fa
rfguided ${TRegGA_DIR}/assembly/rfguided/SYNONYM-on-TARGET/Makefile_rfguided_SYNONYM-on-TARGET
where ${TRegGA_DIR} is the TRegGA home directory, and SYNONYM and TARGET are appropriately substituted.
Thus
make CHECKONLY=no NUMPROC=16 CULTIVAR='\"DA GANG ZHAN\"' SYNONYM=Dagangzhan -f Makefile_TRegGA-orig ${TRegGA_DIR)/reads/Dagangzhan/Dagangzhan_1.fa
would use 16 processors to prepare the Dagangzhan reads (and do no more).
make CHECKONLY=no NUMPROC=12 CULTIVAR='\"DA GANG ZHAN\"' SYNONYM=Dagangzhan -f Makefile_TRegGA-orig ${TRegGA_DIR)/assembly/denovo/Dagangzhan/Dagangzhan-GF/Dagangzhan-GF.gapfilled.final.fa
would use 12 processors to run the Dagangzhan de novo assembly (preparing the reads, unless already present;
but do no more than the de novo assembly).
make CHECKONLY=no TARGET=NbEL2 REFERENCE=OsjCHR3 FROM=460000 TO=480000 -f Makefile_TRegGA-orig ${TRegGA_DIR}/targets/NbEL2.embl >& err
would produce the files for a new target (NbEL2).
make CHECKONLY=no NUMPROC=8 CULTIVAR='\"DA GANG ZHAN\"' SYNONYM=Dagangzhan TARGET=NbEL2 REFERENCE=OsjCHR3 FROM=460000 TO=480000 -f Makefile_TRegGA-orig >& err
would use 8 processors to run the reference-guided assembly of Dagangzhan on this second target (NbEL2),
using the existing reads and de novo assembly.