[MacPorts] #55076: Create port for MEME Suite

[MacPorts]

#55076: Create port for MEME Suite
----------------------------+-----------------------------
  Reporter:  CharlesEGrant  |      Owner:
      Type:  submission     |     Status:  new
  Priority:  Normal         |  Milestone:
 Component:  ports          |    Version:  2.4.2
Resolution:                 |   Keywords:  science biology
      Port:  memesuite      |
----------------------------+-----------------------------

Comment (by kencu):

 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

--
Ticket URL: <https://trac.macports.org/ticket/55076#comment:1>
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