Blat (v3.4) installation error

Question

[hikik1225]

Dear all,

I'm trying to install an earlier version of BLAT (v 3.4) which is required for AlignGraph. I got the following error when executing 'make' in the blastSRC directory:

cd lib && make make[1]: Entering directory
'/home/..../blatSrc34/blatSrc/lib'  gcc -O  -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o aliType.o -c aliType.c aliType.c:5:19: error: ‘rcsid’ defined but not used [-Werror=unused-const-variable=]  static
char const rcsid[] = "$Id: aliType.c,v 1.4 2003/05/06 07:33:41 kate
Exp $";
                   ^~~~~ cc1: all warnings being treated as errors ../inc/common.mk:58: recipe for target 'aliType.o' failed make[1]: ***
[aliType.o] Error 1 make[1]: LEaving directory
'/home/..../blatSrc34/blatSrc/lib'  makefile:2: recipe for target
'all' failed make: *** [all] Error 2

I followed the README file for installation of BLAT on a Linux. For example, I did the below commands.

echo $MACHTYPE
> x86_64

MACHTYPE=x86_64 
export MACHTYPE   
mkdir ~/bin/$MACHTYPE
export PATH="$PATH:~/bin/x86_64"
source ~/.bash_profile

I'd be grateful if you could help me. Thanks in advance.

My environment is as follows:

Ubuntu 18.04.3 LTS

gcc 7.4.0

[Pierre Lindenbaum]

how about just downloading it ? http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/

[hikik1225]

Thanks for your quick response, but it seems the latest version of BLAT, right? I'd like to install older version of BLAT.

[hikik1225]

Oh, sorry. I found older versions in the link you suggested. http://hgdownload.soe.ucsc.edu/admin/jksrc.archive/

But, even though I downloaded files from the above link, installation did not work well.

[Pierre Lindenbaum]

installation did not work well

what do you mean ?

usually you have to make it executable.

chmod +x blat

[b10hazard]

This link did not work for me. Have these files moved?

[Mensur Dlakic]

I would suggest to remove -Werror switch from your makefile (or ../inc/common.mk). It is very strict to abort compilation if any warning comes up.

[hikik1225]

Thank you for your suggestion. "-Werror" was removed from "common.mk" file in the inc directory. Then, compilation was not stopped by error message, but BLAT is not installed in my Linux yet.

[Mensur Dlakic]

Then, compilation was not stopped by error message, but BLAT is not installed in my Linux yet.

You will need to be more descriptive than that. Unless you have used make install, the compilation itself doesn't install anything. If you know the executable file location, type:

/some/directory/containing/blat

Has the executable been created and does it run? If so, you need to put it in the directory that is in your PATH variable, or add another directory to PATH pointing to the present location of blat.