I am installing amos-3.1.0 assembler in my ubuntu system './configure' works fine but when i run 'make' it gives following error
make[4]: Leaving directory /home/orfaau/Downloads/amos-3.1.0/src/hawkeye'
make[3]: Leaving directory/home/orfaau/Downloads/amos-3.1.0/src/hawkeye'
make[3]: Entering directory /home/orfaau/Downloads/amos-3.1.0/src'
make[3]: Nothing to be done forall-am'.
make[3]: Leaving directory /home/orfaau/Downloads/amos-3.1.0/src'
make[2]: Leaving directory/home/orfaau/Downloads/amos-3.1.0/src'
Making all in doc
make[2]: Entering directory /home/orfaau/Downloads/amos-3.1.0/doc'
make[2]: Nothing to be done forall'.
make[2]: Leaving directory /home/orfaau/Downloads/amos-3.1.0/doc'
make[2]: Entering directory/home/orfaau/Downloads/amos-3.1.0'
make[2]: Leaving directory /home/orfaau/Downloads/amos-3.1.0'
make[1]: Leaving directory/home/orfaau/Downloads/amos-3.1.0'
if anyone can help me get this error corrected please thank you in advance.....
•
written
by
namratapatel183 •
From the details you give in one of your comments, there's nothing wrong with your make or your amos installation. You say that the binaries are created in the bin/ folder, but that you cannot run amos commands like Minimo -h. That's only because the binaries are not in your path (specified in the $PATH environment variable), so you wouldn't be able to run them from any other directory than from the directory they are in. I strongly suspect that when you cd to the bin/ directory of amos and run ./Minimo -h, everything runs fine.
This, in the end, is not at all a bioinformatics question, just a standard UNIX question, and you should look for how to put a binary in your $PATH (several solutions possible depending on your taste), or just launch it giving the exact path to the binary myveryownamosdirectory/bin/Minimo -h.
You should probably run a
make clean
or
make distclean
before you run a ./configure and a regular make as it seems you have already compiled amos, so make doesn't have nothing to do. You should carefully read the INSTALL file that comes with amos.
i have run make distclean but after that also it gives the same error so i dont understand what the problem is
Did ./configure give you any errors?
Did you install all pre-requisites? (as listed here: http://wgs-assembler.sourceforge.net/UsingCeleraAssembler.pdf )
No configure did not give me any errors and yes i have installed all pre requisites
When you say your install "doesn't work", what do you mean? no binaries created? binaries corrupted? something else?
when i run make install binaries are created in bin folder but when i try to run any command for example Minimo --h it gives command not found
It looks like you're trying to run the "global" Minimo command, have you tried running (in the bin folder)
./Minimo --h
?
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are you sure it is an error ?
no it is not an error but i am getting this instruction because of which i am not able to install amos