[maker-devel] Installation in a custom directory

Carson Holt carsonhh at gmail.com
Tue Aug 2 10:09:12 MDT 2016 

The install step is installing the C/Perl shared object bindings for MPI to their final location. I could call that internally to ./Build, but since it can fail, and I also since it is configured to fail on missing Perl dependencies, it is better to run it as the final step.

—Carson



> On Aug 2, 2016, at 10:04 AM, Martin MOKREJŠ <mmokrejs at gmail.com> wrote:
> 
> 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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