Create port for MEME Suite

[CharlesEGrant (Charles E. Grant)]

The MEME Suite is a widely use collection of tools for motif analysis (bioinformatics). This package is developed in the laboratories of Dr. William Noble in the Genome Science Dept. of the University of Washington and Dr. Tim Bailey in the Dept. of Pharmacology at the University of Nevada-Reno. I'm the primary maintainer. We'd like to make the MEME Suite software available through MacPorts. The software is covered by a limited commercial use license: it is freely available for non-commerial use, but must be licensed for commercial use.

[CharlesEGrant (Charles E. Grant)]

Portfile

[kencu (Ken)]

Hello. I took a look. I made some changes to the Portfile to be more consistent with the way MacPorts does things -- fully specifying perl and python version, and adding dependencies for specific version. A couple of changes to the distfile specifications.

Is there a reason that parallel_building was disabled? I turned parallel_building back on, and it seemed to work fine.

I ran into one issue that I couldn't easily solve, though:

Checking Required Perl Modules:
XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT
XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT
XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT

The software builds through without these modules, but I fear it may not work correctly. These modules do not seem to me to be available in MacPorts just yet. Perhaps I'm wrong, and they are available but I'm not looking for the right port. Even if they are not, it's not too difficult to write a port that installs a PERL module. Sadly I have not done that before, so the curve for me is a bit higher than some, perhaps.

I notice also that this port installs a very large number of executables into the ${prefix}/bin directory:

$ ls
alphtype			iupac2meme
ama				jaspar2meme
ama-qvalues			llr
ame				mast
beeml2meme			mast_xml_to_html
centrimo			mast_xml_to_txt
ceqlogo				matrix2meme
chen2meme			mcast
clustalw2fasta			meme
clustalw2phylip			meme-chip
compute-prior-dist		meme-chip_html_to_tsv
compute-uniform-priors		meme-get-motif
create-priors			meme-rename
dreme				meme2alph
dreme_xml_to_html		meme2images
dreme_xml_to_txt		meme2meme
dust				meme_xml_to_html
elm2meme			momo
fasta-center			motif-shuffle-columns
fasta-dinucleotide-shuffle	motiph
fasta-fetch			nmica2meme
fasta-get-markov		plotgen
fasta-grep			pmp_bf
fasta-hamming-enrich		priority2meme
fasta-make-index		psp-gen
fasta-most			purge
fasta-re-match			qvalue
fasta-shuffle-letters		ramen
fasta-subsample			ranksum_test
fasta-unique-names		reconcile-tree-alignment
fimo				reduce-alignment
fisher_exact			remove-alignment-gaps
fitevd				rna2meme
gendb				rsat-retrieve-seq
getsize				rsat-supported-organisms
glam2				scpd2meme
glam2format			sd
glam2html			sites2meme
glam2mask			spamo
glam2psfm			taipale2meme
glam2scan			tamo2meme
glam2scan2html			tomtom
gomo				tomtom_xml_to_html
gomo_highlight			transfac2meme
hart2meme-bkg			uniprobe2meme
hartemink2psp			xsltproc_lite
import-html-template

I'm not presently sure if some of those might collide with the names of other commonly used ports. Is there a possibility that they might go into a libexec directory, and only some of them might be available for general discovery on PATH ? The other thing that is commonly done in these situations is to prefix the name with something unique, and I see the configure script does support doing that...

Here's my revised version of your Portfile, perhaps as a stepping stone, once those missing modules are made as ports. -- Ken

[kencu (Ken)]

Portfile - v.1

[kencu (Ken)]

I don't see your license as a MacPorts accepted one. Do any of these license keywords work for you?

Also, we would need some kind of email address for you to use as maintainer.

[kencu (Ken)]

I tried sudo port test to see how the test run went, and that didn't get too far, I'm afraid:

fatal: making test-suite.log: failed to create  -- many logs
make[3]: *** [test-suite.log] Error 1
make[2]: *** [check-TESTS] Error 2
make[1]: *** [check-am] Error 2
make: *** [test] Error 2

I'll put the log up.

[ryandesign (Ryan Carsten Schmidt)]

The maintainers line isn't right. A bareword in the maintainers line is a MacPorts handle; because you're not a MacPorts committer, you don't have a MacPorts handle. You may list your email address, in obfuscated host:user format, and/or your GitHub handle in @handle format. Ideally, list both, grouped in curly brackets (e.g. maintainers {uw.edu:cegrant @CharlesEGrant}).

[CharlesEGrant (Charles E. Grant)]

New version of Portfile for MEME Suite

[CharlesEGrant (Charles E. Grant)]

I've finally been able to get back to make another stab at this. I have attached a new version of a Portfile for the MEME Suite. I think I've addressed all the issues raised by the commenters.

Thanks!

Charles

[CharlesEGrant (Charles E. Grant)]

In a5d4fc03daf42885d0b308dadfa2aca59a5cbad3/macports-ports (master):

memesuite: Portfile submission

The MEME Suite is a widely use collection of tools for motif analysis (bioinformatics). This package is developed in the laboratories of Dr. William Noble in the Genome Science Dept. of the University of Washington and Dr. Tim Bailey in the Dept. of Pharmacology at the University of Nevada-Reno. I'm the primary maintainer. We'd like to make the MEME Suite software available through MacPorts. The software is covered by a limited commercial use license: it is freely available for non-commerial use, but must be licensed for commercial use.

Closes: #55076