[maker-devel] Problem installing maker

Daniel Ence dence at genetics.utah.edu
Tue Jan 21 10:45:32 MST 2014 

Hi Carlos, That message looks like maker installed correctly. Have you tried running it in MPI now? The command to use MPI for maker will look something like "mpiexec -n X maker" where X is the number of processors you want it to use.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of carlos vargas [charlos9 at gmail.com]
Sent: Tuesday, January 21, 2014 10:39 AM
To: Barry Moore
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Problem installing maker

Hi Barry,

Thank you for you help. I got maker running, however when I try to install it with MPI support I face some issues. I installed MPICH2 and performed the test that comes with the package and it went smoothly, however when I try to install maker the following messages appear.


Thank you in advance,

Carlos

~/maker/src$ perl Build.PL

MAKER supports distributed parallelization via MPI.
Would you like to configure MAKER for MPI (This
requires that you have an MPI client installed)? [N ]y

Please specify the path to 'mpicc' on your system: [/usr/bin/mpicc ]
/usr/bin/mpicc

Please specify the path to the directory containing 'mpi.h': [/usr/include/mpi ]
/usr/include/mpi

Would you like to install the web interface to MAKER (MWAS) on this machine
This requires that you be logged in as root or use sudo for './Build install'? [N ]
N
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'MAKER' version '2.3'


The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 2.3
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK


Important Commands:
./Build installdeps #installs missing PERL dependencies
./Build installexes #installs all missing external programs
./Build install #installs MAKER
./Build status #Shows this status menu

Other Commands:
./Build repeatmasker #installs RepeatMasker (asks for RepBase)
./Build blast #installs BLAST (NCBI BLAST+)
./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
./Build snap #installs SNAP
./Build augustus #installs Augustus
./Build apollo #installs Apollo
./Build gbrowse #installs GBrowse (must be root)
./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
./Build webapollo #installs WebApollo (use maker2wap to create DBs)
./Build mpich2 #installs MPICH2 (but manual install recommended)
~/maker/src$ ./Build install
Configuring MAKER with MPI support
Installing MAKER...
Configuring MAKER with MPI support
Subroutine dl_load_flags redefined at (eval 93) line 8.
Installing /home/cvargas/maker/src/../perl/lib/MAKER/ConfigData.pm
Skip /home/cvargas/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.014002 (unchanged)




On Mon, Jan 13, 2014 at 10:21 PM, Barry Moore <barry.utah at gmail.com<mailto:barry.utah at gmail.com>> wrote:
Hi Carlos,

Did you run ./Build install?  If not do that first and then you want to run the copy of maker in ~/software/maker/bin/maker.

B

On Jan 13, 2014, at 1:00 PM, carlos vargas wrote:

Hello,

I have been trying to install maker but I've been facing several issues. After installing all of the prerequisites I ran perl Build.PL and ./Build install. No issues were detected. Afterwards I tried to test maker by simply executing maker -h and got the following error:

Can't locate MAKER/ConfigData.pm in @INC (@INC contains: ~/software/maker/src/bin/../perl/lib ~/software/maker/src/bin/../lib ~/software/maker/src/bin/../src/inc/perl/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at ~/software/maker/src/bin/maker line 42.
BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line 42.

I found a similar thread which suggested reinstalling (which I did) but I still face the same issue. The full messages are below.


Thank you for your help!

Carlos


~/software/maker/src$ sudo perl Build.PL

MAKER supports distributed parallelization via MPI.
Would you like to configure MAKER for MPI (This
requires that you have an MPI client installed)? [N ]
N

Would you like to install the web interface to MAKER (MWAS) on this machine
This requires that you be logged in as root or use sudo for './Build install'? [N ]
N
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'MAKER' version '2.3'


The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 2.3
==============================================================================
PERL Dependencies:      VERIFIED
External Programs:      VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:            DISABLED
MWAS Web Interface:     DISABLED
MAKER PACKAGE:          CONFIGURATION OK


Important Commands:
        ./Build installdeps     #installs missing PERL dependencies
        ./Build installexes     #installs all missing external programs
        ./Build install         #installs MAKER
        ./Build status          #Shows this status menu

Other Commands:
        ./Build repeatmasker    #installs RepeatMasker (asks for RepBase)
        ./Build blast           #installs BLAST (NCBI BLAST+)
        ./Build exonerate       #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
        ./Build snap            #installs SNAP
        ./Build augustus        #installs Augustus
        ./Build apollo          #installs Apollo
        ./Build gbrowse         #installs GBrowse (must be root)
        ./Build jbrowse         #installs JBrowse (MAKER copy, not web accecible)
        ./Build webapollo       #installs WebApollo (use maker2wap to create DBs)
        ./Build mpich2          #installs MPICH2 (but manual install recommended)

~/software/maker/src$ sudo ./Build install
Building MAKER
Installing MAKER...
Building MAKER
Installing ~/software/maker/src/../perl/lib/MAKER/ConfigData.pm

~/software/maker/src$ maker -h
Can't locate MAKER/ConfigData.pm in @INC (@INC contains: ~/software/maker/src/bin/../perl/lib ~/software/maker/src/bin/../lib ~/software/maker/src/bin/../src/inc/perl/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at ~/software/maker/src/bin/maker line 42.
BEGIN failed--compilation aborted at ~/software/maker/src/bin/maker line 42.


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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543<tel:%28801%29%20585-3543>





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