-------- Original Message --------
Subject: Re: FASTX-Toolkit installation
Date: Tue, 28 Apr 2009 14:53:21 -0400
From: Assaf Gordon <gordon@cshl.edu>

... wrote, On 04/28/2009 02:30 PM:
> I'm trying to install the fastx-toolkit on my Mac Leopard workstation.  
> Ultimately, I'd like to integrate it into my local copy of Galaxy.
>
> However, I ran into a snag trying to compile the latest version.  I was able to configure, 
> make and install libgtextutils-0.1.  At least there were no errors after I did that.  
> However, I run into the following when trying to configure fastx-toolkit-0.0.7:
>
>     checking for pkg-config... /sw/bin/pkg-config
>     checking pkg-config is at least version 0.9.0... yes
>     checking for GTEXTUTILS... configure: error: Package requirements
>     (gtextutils-0.1) were not met:
>
>     No package 'gtextutils-0.1' found
>
>     Consider adjusting the PKG_CONFIG_PATH environment variable if you
>     installed software in a non-standard prefix.
>
>     Alternatively, you may set the environment variables GTEXTUTILS_CFLAGS
>     and GTEXTUTILS_LIBS to avoid the need to call pkg-config.
>     See the pkg-config man page for more details.
>
>     gen-biocomp-lp:fastx_toolkit-0.0.7 lparsons$ make
>     make: *** No targets specified and no makefile found.  Stop.
>
>
> Any suggestions would be appreciated.
>


The short answer is that you probably need to set the environment
variable PKG_CONFIG_PATH, like so:
  $ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH

Before running FASTX's "configure" script.


But there's also the long answer:

When you run a standard "./configure" script, the default installation
path is "/usr/local". On some systems (mostly debian/ubuntu), the
default path for most programs is just "/usr" (without "local").

On the other hand, some system administrators like the separation of
'standard' packages into "/usr" and manually built packages into
"/usr/local".

I'm telling you that because it is likely that "gtextutils" was
installed into "/usr/local", but you system doesn't look there at all.

So here's how to check:
go back to the gtextutil directory.
Assuming you already run "configure" + "make", run "make install" as a
REGULAR user (not root).
This will surely fail, but you will see the path, where the installation
process tried to put the library files.
Make a note if the path starts with /usr/local or just /usr (or
strangely - something else).

The installation of GTEXTUTILS puts a file (named "gtextutils-0.1.pc")
somewhere on you disk.
On my computer, it is found on:
  /usr/local/lib/pkgconfig/gtextutils-0.1.pc

The program "pkg-config" is a standard program which reads those ".pc"
files and tells the compiler how to use the library (and it is used by
"configure").

From the command line, run:
  $ pkg-config --cflags gtextutils-0.1

If your file was installed into "/usr/local/lib..." but pkg-config shows
the following error:
  Package gtextutils-0.1 was not found in the pkg-config search path.
  Perhaps you should add the directory containing `gtextutils-0.1.pc'
  to the PKG_CONFIG_PATH environment variable
  No package 'gtextutils-0.1' found

It is like that pkg-config simply doesn't look in "/usr/local/" for the
needed files.

The solution is set a special environment variable, that will instruct
pkg-config where to look:
  $ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
  $ pkg-config --cflags gtextutils-0.1
  -I/usr/local/include/gtextutils-0.1/

Setting "PKG_CONFIG_PATH" to where the ".pc" file is stored will help
the configure process find this library.
After running the "export PKG_CONFIG_PATH" (and assuming the pkg-config
command succeeded), you should be able to run FASTX's "./configure"
successfully.

------

A different solution is to configure GTEXTUTILS to be installed in
"/usr" to begin with (and then, most of the PATH related problems should
be gone).
To do this, run:
    $ ./configure --prefix=/usr
    $ make
    $ sudo make install

In the GTEXTUTILS directory.

------

I hope these tips were helpful.
If you still encounter problems, please let me know.

-Gordon.