Installing a Program called MAQ (Beginner Here)

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1

Basically, I'm trying to install this program called MAQ.

Maq User's Manual

I've downloaded it and I tried to type in $ ./configure; make; make install

but the ouput I got was this:

bash: ./configure: No such file or directory
make[1]: Entering directory `/home/vlay/bwa-0.5.0'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/vlay/bwa-0.5.0'
make[1]: Entering directory `/home/vlay/bwa-0.5.0/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwt_gen.c -o bwt_gen.o
make[1]: gcc: Command not found
make[1]: *** [bwt_gen.o] Error 127
make[1]: Leaving directory `/home/vlay/bwa-0.5.0/bwt_gen'
make: *** [lib-recur] Error 1
make: *** No rule to make target `install'.  Stop.

I'm not sure what any of that really means. I'm also using Cygwin, but again I don't know if that matters.

Thanks for all the help. I'm still really new to all this.

2

You're not going to get very far without a C compiler installed. :slight_smile: Or, if you do have one, it's not in your path.

3

What is that? And how would I get it?

Thanks.

4

It's the program that converts and bundles .c files into executable files. It's necessary to compile most UNIX programs. You'd get that the same way you installed cygwin -- its installer handles other packages too.

5

I'm not entirely sure if I got the C Compiler from Cygwin's installer. Which one should I be looking for?

I keep trying to install MAQ and it says that

"./configure: No such file or directory"

6

It means what it says, there's no file named ./configure in the current directory. The ./configure script is only there by tradition, some things have a completely different build procedure, and the website may be out of date; check any readme's or INSTALL files the download came with first. And from what you posted earlier, you already have a makefile, so try running 'make' again.

As for what you need, 'gcc4', 'gcc4-core', 'gcc4-g++', and 'gcc4-runtime' should get you a compiler, though ideally just gcc4 should pull in the things you need. You may also need headers for whatever libraries maq requires.

7

Ok,

I got the gcc things you listed, but ./configure still said the same thing about no such file or directory

I then tried just typing make but I got this error

$ make
make[1]: Entering directory `/home/vlay/download/bwa-0.5.0'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/vlay/download/bwa-0.5.0'
make[1]: Entering directory `/home/vlay/download/bwa-0.5.0/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwt_gen.c -o bwt_gen.o
bwt_gen.c:1: sorry, unimplemented: 64-bit mode not compiled in
make[1]: *** [bwt_gen.o] Error 1
make[1]: Leaving directory `/home/vlay/download/bwa-0.5.0/bwt_gen'
make: *** [lib-recur] Error 1

Also the program didn't come with a readme file :confused:

8

Well that's progress, of a sort; you now have a working C compiler. :slight_smile: It's just objecting to the strange options the current makefile tries to use it with.

Tell me what 'ls -l' shows. There may be a script you're supposed to run to generate a new makefile.

You could also try removing all instances of '-m64' from the makefile(s), or replacing them with -m32, which may work. It'll compile as 32-bit, but you would appear to have a 32-bit OS anyway.

9

Ahh, its all good now haha. I got it!

Thanks though!