MAKER genome annotation installation help

Question

[bioinformaticssrm2011]

Hello Users,

i new to programming, I am using Ubuntu OS, I tried to install MAKER genome annotation software in it, and got many error because of many dependencies.

I really need to install this software, please tell me how to install it from the beginning, so that there won't be any error.

Best!

Shashank

[GouthamAtla]

Install all the dependencies separately. and post the errors you see.

Answer 1

[st.ph.n]

Form the maker Install file, you can run these commands and all dependencies should be installed for you:

EASY INSTALL

1. Go to the .../maker/src/ directory and run perl Build.PL to configure.
2. Accept default configuration options by just pressing enter. See MPI INSTALL in next section if you decide to configure for MPI.
3. Type ./Build install to complete the installation.

4. If anything fails, either use the ./Build file commands to retry the failed section (i.e. ./Build installdeps and ./Build installexes) or follow the detailed install instructions in the next section to manually install missing modules or programs. Use ./Build status to see available commands.

   ./Build status         #Shows a status menu
   ./Build installdeps    #installs missing PERL dependencies
   ./Build installexes    #installs missing external programs
   ./Build install        #installs MAKER
   

   Note: You do not need to be root. Just say 'yes' to 'local install' when running ./Build installdeps and dependencies will be installed under .../maker/perl/lib, also missing external tools will be installed under .../maker/exe when running ./Build installexes.

   Note: For failed auto-download of external tools, when using the command ./Build installexes, the .../maker/src/locations file is used to identify download URLs. You can edit this file to point to any alternate locations.

[bioinformaticssrm2011]

I give it a try, I start from the beginning, if I encounter any error, I let you know.

Thanks

[bioinformaticssrm2011]

I tried, I guess everything is installed, but one, i.e.

./Build mpich2
ERROR: Failed installing mpich2, now cleaning installation path...
You may need to install mpich2 manually.
[root@root src]# ./Build status
==============================================================================
STATUS MAKER v2.31.8
==============================================================================
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)

I tried to install it manually, but not able to install it.

Any help

[Michael]

Ubuntu has a package for mpich2, try to install via sudo apt-get install mpich2 if you need it.

http://packages.ubuntu.com/trusty/mpich2

[bioinformaticssrm2011]

I tried in my other system as well ubuntu

==============================================================================
STATUS MAKER v2.31.8
==============================================================================
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)

When I typed

./Build install

everything worked good without error. But when I used

maker -help

no command found