[maker-devel] Installation in a custom directory
Sebastien Moretti
I try to install maker in a custom directory following regular Perl
commands with Build.PL.
Unfortunately if I use
perl Build.PL --installdirs=<my_path>
then
./Build install --destdir=<my_root_path>
build install fails with the error:
Can't use an undefined value as a HASH reference at
.../Module/Build/Base.pm line 3038.
It does not happen if I don't use --installdirs
Is there an "official" way to install maker in a custom directory?
Also I found typos in the description of maker at
http://www.yandell-lab.org/software/maker.html
ouputs should be outputs
seusequent should be ???
maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2
Regards
--
Sébastien Moretti
Staff Scientist
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.org/
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Carson Holt
—Carson
Carson Holt
—Carson
> On Aug 2, 2016, at 5:57 AM, Sebastien Moretti <sebastie...@unil.ch> wrote:
>
> OK, just need to move the maker/bin folder.
>
> Thanks
Sebastien Moretti
Thanks
> MAKER will by default put executables in …/maker/bin. You should put …/maker/bin into your PATH. The maker Build.PL is configured to install things in a set directory configuration to properly locate perl libraries, C shared objects, and data files.
sebastie...@unil.ch
README RELEASE
and it looks to be fine.
Thanks
Martin MOKREJŠ
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".
Martin
Sebastien Moretti wrote:
> OK, just need to move the maker/bin folder.
>
> Thanks
>
>> MAKER will by default put executables in …/maker/bin. You should put …/maker/bin into your PATH. The maker Build.PL is configured to install things in a set directory configuration to properly locate perl libraries, C shared objects, and data files.
>>
>> —Carson
>>
>>
>>
>>> On Jul 12, 2016, at 2:35 AM, Sebastien Moretti <sebastie...@unil.ch> wrote:
>>>
>>> Hi
>>>
>>> I try to install maker in a custom directory following regular Perl
>>> commands with Build.PL.
>>>
>>> Unfortunately if I use
>>> perl Build.PL --installdirs=<my_path>
>>> then
>>> ./Build install --destdir=<my_root_path>
>>> build install fails with the error:
>>> Can't use an undefined value as a HASH reference at
>>> .../Module/Build/Base.pm line 3038.
>>>
>>> It does not happen if I don't use --installdirs
>>>
>>>
>>> Is there an "official" way to install maker in a custom directory?
_______________________________________________
Carson Holt
—Carson
Martin MOKREJŠ
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 <mmok...@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
Carson Holt
—Carson