Wrong building path

[wang jenny]

I installed MEME in /clusterdata/uqywan30/meme for the first time, then removed the whole folder.

I installed MEME for the second time in  /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1.

When I ran meme, it hits error like this. My question is how to correct the building path and what's the correct way to remove meme.

Thanks!

Can't locate PriorUtils.pm in @INC (@INC contains: /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin /clusterdata/uqywan30/meme/lib/perl /opt/perl/lib/site_perl/5.14.2/x86_64-linux-thread-multi /opt/perl/lib/site_perl/5.14.2 /opt/perl/lib/5.14.2/x86_64-linux-thread-multi /opt/perl/lib/5.14.2 .) at /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin/psp-gen line 37.

[cegrant]

Hi Jenny,

Several important paths get hardcoded into the applications when  your run configure. If you need to change the installation location you'll need to follow the following steps:

1. cd to the distribution directory
   
2. run 'make clean'
   
3. run './configure' providing the new installation destination using the '--prefix'command
   
4. run 'make'
   
5. run 'make test'
   
6. run 'make install'
   

The old installation directory can simply be removed.

Don't forget to update the PATH environment variable with the location of the new bin directory for the MEME Suite.

[wang jenny]

[uqywan30@cluster meme_4.10.1_install]$ make clean

make: *** No rule to make target `clean'.  Stop.

if there is no make clean, how to clean previous configuration.

[CharlesEGrant]

Something's amiss if you are getting that message. Is that the directory you originally ran 'configure' and 'make' in? Does it contain a file named 'config.log'? If so, please attach a copy of that file.

 

[wang jenny]

I deleted the whole folder. and plan to install again. I run make clean in the new install folder(right after tar).

Is there a way to clean previous configure after deletion of previous installation? Thank you.

[cegrant]

The purpose of 'make clean' is to remove any object or other intermediate files that were left behind by the previous run of 'make'. If you've deleted the distribution directory and created a new one from the tar file there isn't any need to run 'make clean', and in fact none of the 'make' targets can run until you've run './configure'. You can simply remove the previous install directory too. After you've installed to the new location be sure to update the value of your PATH environment variable.

[wang jenny]

I did what you said. It just could make it.

Please refer to my previous question. It hasn't been solved. Thank you very much.

https://groups.google.com/d/msg/meme-suite/Apz8Xk3HC1M/o9F4IvGhCSQJ

[CharlesEGrant]

Please run the following commands and post the results:

echo $PATH

which -a meme

[wang jenny]

Thank you for following my question.

[uqywan30@cluster meme_4.10.1_install]$ echo $PATH

/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin:/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/maven/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/lx26-amd64:/clusterdata/uqywan30/bin

[uqywan30@cluster meme_4.10.1_install]$ which -a meme

/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin/meme

/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin/meme

[cegrant]

Hi Jenny,

Your path contains two copies of the path to the MEME directory, but that shouldn't cause a problem. The location of the MEME directory seems to match the location you specified on your configuration line, so if the install command worked, that should have fixed the problem. Did the 'make install' step report any problems? Do you have permission to write into that directory? Let's try this from the top, recording the results at each step:

./configure --prefix=/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1 --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt

make &> make.log

make test &> test.log

make install &> install.log

meme &> meme.txt

Then forward us copies of config.log, make.log, test.log, install.log, and meme.txt

Charles