-------- Original Message --------
Subject: Re: fastx-toolkit lib path
Date: Thu, 07 May 2009 20:19:34 -0400
From: Assaf Gordon <gordon@cshl.edu>

... wrote, On 05/07/2009 11:33 AM:
> Hi,
>
>   I have just updated my local Galaxy install. 
>   I have noted that some of the tools from the fastx-toolkit are already integrated in the distribution. 
>   So I was wondering about the best way to get them all installed?
>
>   I downloaded and installed *libgtextutils-0.1*, then I tried to install *fastx-toolkit* but 
>   I got many compilation errors which I tried to fix but without success. 
>   I have performed the classic cycle: ./configure ; make ; make install for gtexutils. 
>   In the case of fastx-toolkit I performed ./configure  then when trying the make, I get:
>
> ......
> g++  -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1   -o fasta_formatter fasta_formatter.o /usr/local/include ../libfastx/libfastx.a
> /usr/local/include: file not recognized: Is a directory
> collect2: ld returned 1 exit status
> make[3]: *** [fasta_formatter] Error 1
> make[3]: Leaving directory `/tools/bioinfo/app/galaxy.02.03.09/tmp/fastx_toolkit-0.0.7/src/fasta_formatter'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/tools/bioinfo/app/galaxy.02.03.09/tmp/fastx_toolkit-0.0.7/src'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/tools/bioinfo/app/galaxy.02.03.09/tmp/fastx_toolkit-0.0.7'
> make: *** [all] Error 2
>
>
> Any suggestion to solve properly that problem?
>

Hello,

The default convention (of all GNU-style projects), running:
   ./configure
   make
   make install
will install the package to "/usr/local".
That is - binaries will go to "/usr/local/bin", header files to "/usr/local/include", libraries to "/usr/local/lib".

It seems you are trying to install the files to a different directory (not starting with "/usr/local/" prefix).

This is perfectly fine, but the correct way to do it is to use the "prefix" parameter to the "./configure" script, as such:

   $ ./configure --prefix=/tools/bioinfo/app/
   $ make
   $ sudo make install

This will install the binaries to "/tools/bioinfo/app/bin", etc.

If you use the "prefix" option to build the GTEXTUTILS library, it will be installed to "/tools/bioinfo/app/lib".
But be away - the building process of FASTX-Toolkit doesn't know to look in "/tools/bioinfo/app/lib" for the library - and it will fail.

The way to fix that is to use the PKG_CONFIG_PATH variable, to tell the configure script where to look for the library, as such:

 ##
 ## Build the library, install to "/tools/bioinfo/app"
 ##
 $ cd gtextutils-0.1
 $ ./configure --prefix=/tools/bioinfo/app
 $ make
 $ sudo make install
 $ cd ..
 ##
 ## Build the FASTX-Toolkit, install to "/tools/bioinfo/app"
 ##  and instruct pkg_config to look in "/tools/bioinfo/app"
 ##  for the libraries
 $ cd fastx-toolkit-0.8
 $ export PKG_CONFIG_PATH=/tools/bioinfo/app/lib/pkgconfig
 $ ./configure --prefix=/tools/bioinfo/app
 $ make
 $ sudo make install


Regards,
   Gordon.