[maker-devel] Problem installing maker
carlos vargas
charlos9 at gmail.com
Tue Jan 21 10:39:03 MST 2014
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> 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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> maker-devel at box290.bluehost.com
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>
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>
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