I have a problem to train my data with GlimmerHMM. The manual says:
But when I run make in this directory (I am not the administrator but I have rights to execute and read), I get this:
I thought that was everything in order but when I run my command line:
I receive:
I saw that other people already manage to train with their data. Could someone explain how you did it? Or how to solve this?
I think that something is wrong in the makefile:
How have you the makefile?
Thanks!
Train GlimmerHMM module.
To use this trainning module, first run make in this directory, and than call
trainGlimmerHMM with the parameters specified below.
Usage:
trainGlimmerHMM <mfasta_file> <exon_file> [optional_parameters]
To use this trainning module, first run make in this directory, and than call
trainGlimmerHMM with the parameters specified below.
Usage:
trainGlimmerHMM <mfasta_file> <exon_file> [optional_parameters]
Code:
make: Nothing to be done for `all'.
Code:
trainGlimmerHMM sequence.mfasta trainingdata.txt
Code:
trainGlimmerHMM: command not found
I think that something is wrong in the makefile:
# Copyright (c) 2003 by Mihaela Pertea.
# C compiler
C = gcc
CC = g++
CFLAGS = -O1 ${SEARCHDIRS}
#CFLAGS = -O3 -g -Wall
LIBS = -lm
MAKEFILE= makefile
.PHONY : all
all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin score score2 scoreATG scoreATG2 scoreSTOP scoreSTOP2 erfapp splicescore
# C compiler
C = gcc
CC = g++
CFLAGS = -O1 ${SEARCHDIRS}
#CFLAGS = -O3 -g -Wall
LIBS = -lm
MAKEFILE= makefile
.PHONY : all
all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin score score2 scoreATG scoreATG2 scoreSTOP scoreSTOP2 erfapp splicescore
Thanks!
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