Blat installation

[ronaldrcutler]

Hello all,

I have been using AlingGraph to aling contigs I have to a reference genome. This program uses blat, however only supports up to version 34. I downloaded the blatSrc34.zip source code file and followed the README for installation on a Mac OSX 10.10.5. I get this error when executing the last step by running the make file using 'make' in the blastSRC directory:

$ make

cd lib && /Applications/Xcode.app/Contents/Developer/usr/bin/make

gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -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: unused variable 'rcsid' [-Werror,-Wunused-const-variable]

static char const rcsid[] = "$Id: aliType.c,v 1.4 2003/05/06 07:33:41 kate Exp $";

^

1 error generated.

make[1]: *** [aliType.o] Error 1

make: *** [all] Error 2

Any help with this?

[GenoMax]

Are you sure about the requirement for v34? Have you tried the latest blast executable for Mac OS?

[ronaldrcutler]

Steps to install blat v34 on Mac OSX (10.10.5)

This is for Mac users who are using AlignGraph and want to use blat alignment which requires blat v34 (latest at the time of writing is blat v36)

Credit goes to Maximilian Haeussler & Hiram Clawson from blat for their help.

Download zip from the blat archives
Unzip folder (blatSrc) and place in desired directory

*replace ar rcus in lib/makefile with libtool -static -o
*replace ar rcus $(T) $(O) in jkOwnLib/makefile with libtool -static -o $(T) $(O)

1. Check that the environment variable MACHTYPE exist on your system.

command: $echo $MACHTYPE
my result: x86_64-apple-darwin14

2. Determine what system reports itself as:

$uname -m
my result: x86_64

3. Set the MACHTYPE environment variable in ~/.bash_profile

open ~/.bash_profile: $open -a TextEdit ~/.bash_profile

write this: MACHTYPE=x86_64
write this: export MACHTYPE

close and save profile and then update: $source ~/.bash_profile

4. Make the directory ~/bin/$MACHTYPE where (non-web) executables will go.

$mkdir /usr/local/bin/$MACHTYPE

5. Add the directory made above to the path. In ~/.bash_profile similar to step 3

write this: PATH=$PATH:/usr/local/bin/$MACHTYPE

6. Make the directory $MACHTYPE in the lib directory (if not there already)

$mkdir /usr/local/bin/blastsrc/lib/$MACHTYPE

7. create jkweb in lib directory

lib$ make HG_WARN=""

8. In the blastSrc directory type 'make'

blastSrc$ make HG_WARN=''"

If you get this error:

ld: can't open output file for writing: /Users/*your_username/bin/x86_64/blat, errno=2 for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [blat] Error 1
make: *** [all] Error 2

Than go ahead and make the directory:

$ mkdir /Users/*your_username/bin/x86_64

The executable will be output in your directory. In this case you will have to go back in your ~/.bash_profile and change the path in order to use the executables easily in the ternimal.

Cheers