Question: BLAT installation *** No rule to make target '../lib//jkweb.a', needed by 'blat'
0
gravatar for marongiu.luigi
22 days ago by
Germany, Mannheim, UMM
marongiu.luigi120 wrote:

Dear all,

I am trying to install BLAT. As specified in the README file that accompanies the package I created the folder ~/bin/$MACHTYPE.

My MACHTYPE variable is

x86_64-pc-linux-gnu

which matches with the directory blatSrc/lib/x86_64 contained in BLAT. I added ~/bin/x86_64-pc-linux-gnu to the PATH. The BLAT directory (blatSrc) is in /usr/local/lib/ but when i ran the make command i got:

/usr/local/lib/blatSrc $ sudo make
cd lib && make
make[1]: Entering directory '/usr/local/lib/blatSrc/lib'
make[1]: '/jkweb.a' is up to date.
make[1]: Leaving directory '/usr/local/lib/blatSrc/lib'
cd jkOwnLib && make
make[1]: Entering directory '/usr/local/lib/blatSrc/jkOwnLib'
make[1]: '../lib//jkOwnLib.a' is up to date.
make[1]: Leaving directory '/usr/local/lib/blatSrc/jkOwnLib'
cd blat && make
make[1]: Entering directory '/usr/local/lib/blatSrc/blat'
make[1]: *** No rule to make target '../lib//jkweb.a', needed by 'blat'.  Stop.
make[1]: Leaving directory '/usr/local/lib/blatSrc/blat'
makefile:2: recipe for target 'all' failed
make: *** [all] Error 2

I found that MACHTYPE should not have dashes so I changed the folder to ~/bin/x86_64 (again in the PATH) and I ran:

MACHTYPE=x86_64
export $MACHTYPE

but I got the following:

 /usr/local/lib/blatSrc  $ sudo make
cd lib && make
make[1]: Entering directory '/usr/local/lib/blatSrc/lib'
make[1]: '/jkweb.a' is up to date.
make[1]: Leaving directory '/usr/local/lib/blatSrc/lib'
cd jkOwnLib && make
make[1]: Entering directory '/usr/local/lib/blatSrc/jkOwnLib'
make[1]: '../lib//jkOwnLib.a' is up to date.
make[1]: Leaving directory '/usr/local/lib/blatSrc/jkOwnLib'
cd blat && make
make[1]: Entering directory '/usr/local/lib/blatSrc/blat'
make[1]: *** No rule to make target '../lib//jkweb.a', needed by 'blat'.  Stop.
make[1]: Leaving directory '/usr/local/lib/blatSrc/blat'
makefile:2: recipe for target 'all' failed
make: *** [all] Error 2

Same thing if i do export MACTYPE. I also tried with make MACHTYPE=$MACHTYPE as reported, but same error.

Could you tell me what I am getting wrong?

Thank you

assembly software error • 165 views
ADD COMMENTlink modified 22 days ago • written 22 days ago by marongiu.luigi120

Does BLAT make call for a sudo? It is very uncommon for software to need sudo to make anything.

ADD REPLYlink written 22 days ago by Ram13k

I use sudo because of the privileged location /usr/... when building without privileges I sometimes got problems with writing permissions. anyhow even with make only I got the same error.

ADD REPLYlink written 22 days ago by marongiu.luigi120
1

You should never sudo make. If you have exported variables, they are not passed on through make because a new shell is opened for make targets. If you need to pass on variables through sudo, which might be the case for building and installing cpan modules globally, e.g. those that link against the kent-source tree containing jkweb.a, you can and have to do it like so:

sudo MACHTYPE=x86_64 cpan Bio::DB::SAM
or 
sudo -E cpan

but this is only for commands where you can't separate the build from the install process.

ADD REPLYlink modified 22 days ago • written 22 days ago by Michael Dondrup43k

This belongs in a comment, not as an answer. I'll move it to a comment now, but please be more cautious in the future and use the Add Comment or Add Reply (which you've used above) facilities.

ADD REPLYlink written 22 days ago by Ram13k
2
gravatar for Ram
22 days ago by
Ram13k
New York
Ram13k wrote:

Also, you may want to take a look at this: http://nix-bio.blogspot.com/2013/10/installing-blat-and-blast.html

ADD COMMENTlink written 22 days ago by Ram13k

Thank you, the link seems very good. This time i ran:

$ echo $MACHTYPE
x86_64-pc-linux-gnu
$ MACHTYPE=x86_64
$ export MACHTYPE
$ echo $MACHTYPE 
x86_64
$ export PATH=~/bin/x86_64::$PATH
$ make

and the following files are created in ~/bin/x86_64/

$ ls
blat     faToTwoBit  gfServer  pslPretty  pslSort     twoBitToFa
faToNib  gfClient    nibFrag   pslReps    twoBitInfo

I refreshed the PATH variable with source ~/.bashrc and then I ran

$ blat
blat - Standalone BLAT v. 35 fast sequence search command line tool

So I'd say the problem is solved. Thanks again.

ADD REPLYlink written 22 days ago by marongiu.luigi120

Great, glad to know.

If the answer was helpful, upvote it, if it resolved your question, mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 22 days ago by Ram13k
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