[maker-devel] Installation in a custom directory

Martin MOKREJŠ mmokrejs at gmail.com
Tue Aug 2 10:04:05 MDT 2016 

Hi Carson,

Carson Holt wrote:
> You are probably thinking of times you have used Build.PL for installing modules (primarily from CPAN). MAKER is not a module. You should really think of Build.PL as being akin to a Perl version of ‘make’. Just like ‘make', Build.PL can be configured to do the necessary configuration/setup for nearly anything. In this case, it’s not installing a module, rather Build.PL is just configuring external dependencies for a package of scripts. So the options you are trying to configure for have no meaning given how Build.PL is set up in this case.

Maybe I was fooled by the install step.

>
> —Carson
>
>
>> On Aug 2, 2016, at 9:29 AM, Martin MOKREJŠ <mmokrejs at gmail.com> wrote:
>>
>> Hi Sebastien,
>>  I had similar concerns in the past as well.
>>
>>  I also would like to install it elsewhere, but usually Build.PL works with other packages. This is not the case of maker.
>>
>>  I would also would need two or three commandline switches: --destdir=${DESTDIR} --prefix=${EPREFIX}/usr --perl-inc-path=${EPREFIX}/${VENDOR_LIB} --perl-man-path=$somewhereelse
>>
>> From the above, the ${EPREFIX}/usr could be compiled into binaries, config files, etc.
>> The ${DESTDIR} should contain subdirectories /usr, /usr/lib, /usr/share, etc. so that a script could do: cd /my/temp/path; tar cf - . | maker.tgz and later unpack it over my / (root directory) of the filesystem.
>>
>> Then I could finish my abandoned attempt to make a package for maker in Gentoo Linux ( https://cgit.gentoo.org/proj/sci.git/diff/sci-biology/maker/maker-2.31.8.ebuild ), exactly because of these issues. ;-) As you may see, I am especially stuck with what to do with maker/lib/ contents, seems like pre-installed perl apps. I need to create a package for each of them separately before proceeding with "rm -rf maker/lib".


>>> Emerging (1 of 1) sci-biology/maker-2.31.8::science
  * maker-2.31.8.tgz SHA256 SHA512 WHIRLPOOL size ;-) ...                                                                                                                                                                                                                                                                [ ok ]
>>> Unpacking source...
>>> Unpacking maker-2.31.8.tgz to /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work
>>> Source unpacked in /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work
>>> Preparing source in /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src ...
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src ...
>>> Source configured.
>>> Compiling source in /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src ...

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
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'MAKER' version 'v2.31.8'


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


==============================================================================
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)
Building MAKER
Installing MAKER...
Building MAKER
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../perl/lib/MAKER/ConfigData.pm
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../perl/lib/Parallel/Application/MPI.pm
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../perl/man/MAKER::ConfigData.3pm
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/map_fasta_ids
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/cufflinks2gff3
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker2eval_gtf
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/genemark_gtf2gff3
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker2wap
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker_map_ids
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/ipr_update_gff
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker2jbrowse
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker2chado
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/compare
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/fasta_tool
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker_functional
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/iprscan2gff3
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/iprscan_wrap
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/evaluator
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker2zff
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/cegma2zff
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/fasta_merge
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/map_data_ids
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker_functional_fasta
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/chado2gff3
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/gff3_merge
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/tophat2gff3
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/map2assembly
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/map_gff_ids
Installing /scratch/var/tmp/portage/sci-biology/maker-2.31.8/work/maker/src/../bin/maker_functional_gff
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/maker-2.31.8

>>> Install maker-2.31.8 into /scratch/var/tmp/portage/sci-biology/maker-2.31.8/image/ category sci-biology
>>> Completed installing maker-2.31.8 into /scratch/var/tmp/portage/sci-biology/maker-2.31.8/image/

  * Final size of build directory: 40312 KiB
  * Final size of installed tree: 12656 KiB

ecompressdir: bzip2 -9 /usr/share/man
ecompressdir: bzip2 -9 /usr/share/doc

>>> Installing (1 of 1) sci-biology/maker-2.31.8::science
>>> Auto-cleaning packages...




That gives me these files installed on my system:

# equery files maker
  * Searching for maker ...
  * Contents of sci-biology/maker-2.31.8:
/usr
/usr/bin
/usr/bin/cegma2zff
/usr/bin/chado2gff3
/usr/bin/compare_gff3_to_chado
/usr/bin/cufflinks2gff3
/usr/bin/evaluator
/usr/bin/fasta_merge
/usr/bin/genemark_gtf2gff3
/usr/bin/gff3_merge
/usr/bin/ipr_update_gff
/usr/bin/iprscan2gff3
/usr/bin/iprscan_wrap
/usr/bin/maker
/usr/bin/maker2chado
/usr/bin/maker2eval_gtf
/usr/bin/maker2jbrowse
/usr/bin/maker2wap
/usr/bin/maker2zff
/usr/bin/maker_functional
/usr/bin/maker_functional_fasta
/usr/bin/maker_functional_gff
/usr/bin/maker_map_ids
/usr/bin/map2assembly
/usr/bin/map_data_ids
/usr/bin/map_fasta_ids
/usr/bin/map_gff_ids
/usr/bin/tophat2gff3
/usr/lib64
/usr/lib64/perl5
/usr/lib64/perl5/vendor_perl
/usr/lib64/perl5/vendor_perl/5.20.2
/usr/lib64/perl5/vendor_perl/5.20.2/MAKER
/usr/lib64/perl5/vendor_perl/5.20.2/MAKER/ConfigData.pm
/usr/lib64/perl5/vendor_perl/5.20.2/Parallel
/usr/lib64/perl5/vendor_perl/5.20.2/Parallel/Application
/usr/lib64/perl5/vendor_perl/5.20.2/Parallel/Application/MPI.pm
/usr/share
/usr/share/doc
/usr/share/doc/maker-2.31.8
/usr/share/doc/maker-2.31.8/INSTALL.bz2
/usr/share/doc/maker-2.31.8/README.bz2
/usr/share/maker
/usr/share/maker/GMOD
/usr/share/maker/GMOD/Apollo
/usr/share/maker/GMOD/Apollo/gff3.tiers
/usr/share/maker/GMOD/JBrowse
/usr/share/maker/GMOD/JBrowse/maker.css
/usr/share/maker/data
/usr/share/maker/data/dpp_contig.fasta
/usr/share/maker/data/dpp_est.fasta
/usr/share/maker/data/dpp_protein.fasta
/usr/share/maker/data/hsap_contig.fasta
/usr/share/maker/data/hsap_est.fasta
/usr/share/maker/data/hsap_protein.fasta
/usr/share/maker/data/te_proteins.fasta
/usr/share/man
/usr/share/man/man3
/usr/share/man/man3/MAKER::ConfigData.3pm.bz2



$ /usr/bin/maker
Argument "2.49_01" isn't numeric in numeric ge (>=) at /usr/lib64/perl5/vendor_perl/5.20.2/x86_64-linux-thread-multi/forks.pm line 1570.
Can't locate GI.pm in @INC (you may need to install the GI module) (@INC contains: /home/mmokrejs/proj/sci/sci-biology/maker/_Inline/lib /usr/bin/../perl/lib /usr/bin/../lib /usr/bin/../src/inc/perl/lib /etc/perl /usr/local/lib64/perl5/5.20.2/x86_64-linux-thread-multi /usr/local/lib64/perl5/5.20.2 /usr/lib64/perl5/vendor_perl/5.20.2/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.20.2 /usr/local/lib64/perl5 /usr/lib64/perl5/vendor_perl /usr/lib64/perl5/5.20.2/x86_64-linux-thread-multi /usr/lib64/perl5/5.20.2 .) at /usr/bin/maker line 63.
BEGIN failed--compilation aborted at /usr/bin/maker line 63.
$

Of course, because as I said, I need to install properly all the dependencies from maker/lib/ subdirectory.


BTW, did perl Build.PL introduce the _Inline/lib/ directory? It somehow escaped from the sanbox I think. :(

But thank you for you kind answer anyway,
Martin

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