[maker-devel] install maker on cluster

[Carson Holt]

You may need to reconfigure your cpan preferences.

You can do this manually by editing the ~/.cpan/CPAN/MyConfig.pm file, or
by starting cpan from your command line (command is cpan).  Then run 'o
conf init' inside the cpan ui.

--Carson


On 12-10-09 7:07 AM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:

>Hello maker-team,
>
>I am trying to install maker 2.25 on a cluster, without root privileges
>(I managed before, but now after migration to a new cluster I cant seem
>to get it to work). All necessary prerequisite programs are installed
>and in the path (I followed the steps in the INSTALL file that comes
>with maker2.25). When I do:  perl Build.PL, I get:
>Checking prerequisites...
>   requires:
>     !  DBD::SQLite is not installed
>     !  IO::All is not installed
>     !  Inline::C is not installed
>     !  Perl::Unsafe::Signals is not installed
>     !  Proc::ProcessTable is not installed
>     !  Want is not installed
>     !  forks is not installed
>     !  forks::shared is not installed
>   build_requires:
>     !  LWP::Simple is not installed
>   recommends:
>     *  DBD::Pg is not installed
>
>ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
>versions
>of the modules indicated above before proceeding with this installation
>
>Run 'Build installdeps' to install missing prerequisites.
>
>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
>
>WARNING: Apache cannot be located. The optional web based
>interface to MAKER will not be available to you.
>
>Created MYMETA.yml and MYMETA.json
>Creating new 'Build' script for 'MAKER' version '2.25'
>
>
>The file 'Build' has been created for you to finish installing MAKER.
>
>
>==========================================================================
>====
>STATUS MAKER 2.25
>==========================================================================
>====
>PERL Dependencies:      MISSING
>                   !  forks
>                   !  IO::All
>                   !  forks::shared
>                   !  Want
>                   !  DBD::SQLite
>                   !  Proc::ProcessTable
>                   !  Inline::C
>                   !  Perl::Unsafe::Signals
>
>External Programs:      VERIFIED
>External C Libraries:   VERIFIED
>MPI SUPPORT:            DISABLED
>MWAS Web Interface:     DISABLED
>MAKER PACKAGE:          MISSING PREREQUISITES
>
>
>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 mpich2          #installs MPICH2 (but manual install
>recommended)
>
>So it seems some Perl Dependencies are missing. As indicated in INSTALL
>I followed the quick and dirty installation for Bioperl, so I am not
>sure what I did wrong/missed out.
>
>When I run ./Build installdeps, I get:
>You do not have write access to install missing Modules.
>I can try and install these locally (i.e. only for MAKER)
>in the .../maker/perl/lib directory, or you can run
>'./Build installdeps' as root or using sudo and try again.
>Do want MAKER to try and build a local installation? [N ]y
>mkdir /usit/titan: Permission denied at
>/cluster/software/VERSIONS/perlmodules-5.10_1/lib/perl5/CPAN/FTP.pm line
>59
>
>Sorry to bother you with this minor things!! Any help would me much
>appreciated!
>
>much obliged,
>Christoph
>
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