Commit graph

424 commits

Author SHA1 Message Date
asau
5f463c5121 If we have started forcing another Fortran compiler (like for MOPAC7
in biology/mopac), force it here too.
2016-01-03 23:08:34 +00:00
dholland
a3d1589e21 Whitespace. 2015-12-29 04:54:34 +00:00
dholland
b421a108d7 Fix build.
1. Compile C code with the C compiler, not the fortran compiler.
2. Use f2c, not g95, as the fortran compiler.

XXX  This package builds only with f2c, not g95.
XXX  There does not appear to be any way to specify this other
XXX  than by abusively setting PKGSRC_FORTRAN. So do that for now.
2015-12-26 22:36:07 +00:00
wiedi
b15782dd1c Fix network libs on SunOS 2015-12-12 17:26:05 +00:00
wiedi
6a6bdae524 Fix int types and network libs on SunOS 2015-12-12 16:56:04 +00:00
adam
7f3b4730ad Extend PYTHON_VERSIONS_INCOMPATIBLE to 35 2015-12-05 21:25:27 +00:00
dholland
51a3103c47 gets() considered harmful. What is this, 1985? Fixes the build on OpenBSD. 2015-11-07 21:06:37 +00:00
dholland
9e4d91002d Unconditionally uses <emmintrin.h>, so restrict to x86. 2015-11-07 20:20:54 +00:00
agc
bca6c81b27 Add SHA512 digests for distfiles for biology category.
Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
2015-11-02 18:42:20 +00:00
leot
7b83648f44 Add bwa. 2015-10-14 17:13:44 +00:00
leot
ff3972c8c8 Import biology/bwa as bwa-0.7.9a.
Packaged in pkgsrc-wip by Jason Bacon.

BWA is a software package for mapping low-divergent sequences against a large
reference genome, such as the human genome.
2015-10-14 17:12:52 +00:00
leot
408f6ea29e Add cdhit. 2015-10-12 16:49:03 +00:00
leot
2653431fc6 Import biology/cdhit as cdhit-4.6.4.
Packaged in pkgsrc-wip by Jason Bacon.

CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.
2015-10-12 16:48:08 +00:00
asau
0942afe6c3 Skip portability checks for sample scripts. 2015-07-27 19:47:55 +00:00
asau
2ffed7a925 + gabedit 2015-07-22 19:49:07 +00:00
asau
570b76baad Import Gabedit 2.4.8 as biology/gabedit.
Gabedit is a graphical user interface to computational chemistry
packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC,
OpenMopac, Orca, PCGamess and Q-Chem.

It can display a variety of calculation results including
support for most major molecular file formats.
The advanced "Molecule Builder" allows to rapidly sketch in
molecules and examine them in 3D. Graphics can be exported to
various formats, including animations.

Major features

 * Gabedit can create input file for GAMESS(US), GAUSSIAN,
   MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem.
 * Gabedit can graphically display a variety of Gamess-US,
   Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess,
   Q-Chem, (partially) ErgoSCF and (partially) ADF calculation
   results, including the following:
     + Molecular orbitals.
     + Surfaces from the electron density, electrostatic
       potential, NMR shielding density, and other properties.
     + Surfaces may be displayed in solid, translucent and wire
       mesh modes. they are can be colorcoded by a separate property.
     + Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes
       and the principal axes of the molecule.
     + Animation of the normal modes corresponding to vibrational
       frequencies.
     + Animation of the rotation of geometry, surfaces, contours,
       planes colorcoded, xyz and the principal axes of the molecule.
     + Animation of contours, Animation of planes colorcoded.
 * Gabedit can display UV-Vis, IR and Raman computed spectra.
 * Gabedit can generate a povray file for geometry (including
   hydrogen's bond),surfaces (including colorcoded surfaces),
   contours, planes colorcoded.
 * Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format.
 * Gabedit can generate automatically a series of pictures
   for animation (vibration, geometry convergence, rotation, contours,
   planes colorcoded).
 * Simulated Annealing with Molecular Dynamics is implemented in Gabedit
   (using Amber 99 molecular mechanics parameters).
2015-07-22 19:05:10 +00:00
wiz
40bbad7ac6 Comment out dependencies of the style
{perl>=5.16.6,p5-ExtUtils-ParseXS>=3.15}:../../devel/p5-ExtUtils-ParseXS
since pkgsrc enforces the newest perl version anyway, so they
should always pick perl, but sometimes (pkg_add) don't due to the
design of the {,} syntax.

No effective change for the above reason.

Ok joerg
2015-07-12 18:56:06 +00:00
dholland
8269327870 Pass -freal-loops if the compiler is clang or gcc. This does not fix
the build, but it gets further now.
2015-06-27 07:08:13 +00:00
wiz
0982effce2 Recursive PKGREVISION bump for all packages mentioning 'perl',
having a PKGNAME of p5-*, or depending such a package,
for perl-5.22.0.
2015-06-12 10:48:20 +00:00
tnn
255d0cb0b8 Recursive revbump following MesaLib update, categories a through f. 2015-04-25 14:20:17 +00:00
mef
cc535ed362 Use INSTALL_PROGRAM for executables (instead of INSTALL_DATA). 2015-01-31 06:21:39 +00:00
mef
fc96e80a63 Update 2.2.3 to 2.3.6
---------------------
ChangeLog unknown.
2015-01-31 06:18:42 +00:00
mef
5d1643bcbd Update HOMEPAGE, was Host Unknown. But the link to download still gets 404. 2014-12-20 12:02:28 +00:00
joerg
7e52fa03d6 Don't depend on implicit ${PREFIX}/lib. 2014-12-11 22:06:08 +00:00
joerg
67ad55aa8d Adjust !TR1 support again. 2014-11-24 00:47:48 +00:00
joerg
a18826148d Wants pkg-config. 2014-11-21 22:14:52 +00:00
mef
081f03f18c Correction to PLIST when option wx-gui is enabled. 2014-11-20 09:10:32 +00:00
mef
ea926497d1 (upstream) update 2.3.0 to 2.3.2
(ChangeLog)
2012-08-20  Paolo Tosco <paolo.tosco@unito.it>
        * src/formats/mol2format.cpp: added a check for N.4 nitrogens
        (fixes PR#3557898)

2012-06-09  Paolo Tosco <paolo.tosco@unito.it>
        * src/kekulize.cpp: reverted the r4862 patch to kekulize.cpp;
        the incorrect aromaticity perception of oxonium salts concerned
        only the MOL2 format, so the fix was applied to mol2format.cpp
        instead
        * src/formats/mol2format.cpp: added a check to improve downstream
        aromaticity perception on charged molecules containing oxygen

2012-06-07  Paolo Tosco <paolo.tosco@unito.it>
        * include/openbabel/atom.h: added protos for CountFreeSulfurs() and
        IsThiocarboxylSulfur() functions which are equivalent to
        CountFreeOxygens() and IsCarboxylOxygen() and address
        (di)thiocarboxyl groups
        * src/atom.cpp: added the CountFreeSulfurs() and
        IsThiocarboxylSulfur() functions
        * src/forcefields/forcefieldmmff94.cpp: added some additional
        checks to make MMFF94 atom type assignment more robust
        * src/formats/mol2format.cpp: added some checks to improve downstream
        aromaticity perception on charged molecules containing nitrogen,
        oxygen and sulfur
        * src/kekulize.cpp: added a check to fix incorrect perception of
        aromatic oxonium and thionium cations

(NEWS)
Open Babel 2.3.1 (2011-10-14)

This release represents a major bug-fix release and is a stable
upgrade, strongly recommended for all users of Open Babel. Many bugs
and enhancements have been added since the 2.3.0 release.

Citation:

Please consider citing this work if you publish work which used Open Babel:
Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim
Vandermeersch  and Geoffrey R. Hutchison. "Open Babel: An open
chemical toolbox." Journal of Cheminformatics 2011, 3:33.

http://dx.doi.org/10.1186/1758-2946-3-33
2014-11-20 09:05:56 +00:00
wiz
cda18437be Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles. 2014-10-09 14:05:50 +00:00
jperkin
4ef19a60c0 Fix "call of overloaded 'abs(unsigned int)' is ambiguous". 2014-09-23 14:33:40 +00:00
wen
964cd83308 Update to 1.6.924
Upstream changes:
1.6.924

    [Significant changes]

    * Bug/feature issue tracking has moved to GitHub Issues:
          https://github.com/bioperl/bioperl-live/issues
    * DB_File has been demoted from "required" to "recommended",
      which should make easier for Windows users to install BioPerl
      if they don't need that module.

    [New features]

    * Bio::Search::HSP::GenericHSP
        - Bug #3370, added a "posterior_string" method to retrieve the
          posterior probability lines (PP) from HMMER3 reports [fjossandon]
        - Added a "consensus_string" method to retrieve the consensus
          structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
    * Bio::SearchIO::hmmer2
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Query Length and Hit Length are reported when the alignment
          runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
    * Bio::SearchIO::hmmer3
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Hit Length is reported when the alignment runs until the end
          of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
        - Implemented the capture of the posterior probability lines [fjossandon]
        - Completed the development of NHMMER parsing, including alignments [fjossandon]
    * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
        - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
          "min_score", "min_bits, and "hit_filter" methods from
          'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
          This means that the Bio::SearchIO->new() parameters '-signif', '-score',
          '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
          besides Blast, instead of being ignored. Added tests for all moved methods
          using HMMER outputs and run the full test suite and everything pass [fjossandon]
    * Bio::SeqIO::MultiFile
        - Autodetection of file format [fangly]
    * Bio::Tools::GuessSeqFormat:
        - Format detection from non-seekable filehandles such as STDIN [fangly]

    [Bug fixes]

    * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
    * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
    * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
    * Abstract: Fixed ActivePerl incapability of removing temporary files
      because of problems closing tied filehandles [fjossandon]
    * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
      because ActivePerl were producing a ".index.pag" and ".index.dir"
      files instead of a single ".index" file (like Strawberry Perl).
      Now those temporary files are correctly considered and deleted. [fjossandon]
    * Test files: Added missing module requirements (DB_File and Data::Stag)
      to several tests files that were failing because those modules were
      not present. Now those test files are correctly skipped instead. [fjossandon]
    * Blast: Added support to changes in bl2seq from BLAST+ output, which
      now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
    * Phylip: Return undef in "next_aln" at file end to avoid
      an infinite loop [yschensandiego]
    * HMMER3: When a hit description is too long, it is truncated in
      the Scores table. In those cases, the more complete description from
      the Annotation line (>>) will be used [fjossandon]
    * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
      since it is now used by HMMER3 format in alignments [fjossandon]
    * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
      to return undef if the query/hit length is unknown (like in some
      HMMER outputs), to avoid division by 0 crashes. Also "query_length"
      now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
    * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
      added support to multi-query reports, reduced code redundancy,
      and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
    * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
    * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
    * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
    * Fixed some Bio::Root::Utilities subroutines [fjossandon]
    * Double-quotes on paths are needed in some places [fjossandon]
    * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
    * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
    * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
      with the latest changes made in their own repositories [fjossandon]
    * General synching of files with the master branch [fjossandon]
    * Fixed tests failing in Windows because of using Linux commands [fjossandon]
    * Closed many open filehandles that prevented temporary files deletion [fjossandon]
    * Fixed broken MeSH parser [fjossandon]
    * Fixed missing detection of format in SeqIO when given a -string [fangly]
2014-07-17 12:12:26 +00:00
obache
3994080cf7 DB_File was first released with perl 5 2014-06-02 12:51:38 +00:00
obache
78940b3039 perl>=5.19.6 contains Module::Build>0.42
perl>=5.10.1 contains ExtUtils::Manifest>=1.52
perl>=5.8.1 contains Storable>=2.05
2014-06-02 10:06:06 +00:00
wiz
7eeb51b534 Bump for perl-5.20.0.
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.
2014-05-29 23:35:13 +00:00
wiz
c1b44346cd Mark packages that are not ready for python-3.3 also not ready for 3.4,
until proven otherwise.
2014-05-09 07:36:53 +00:00
ryoon
60806aa001 Recursive revbump from x11/pixman
Fix PR pkg/48777
2014-05-05 00:47:34 +00:00
asau
5aac8e7753 __BSD_VISIBLE is needed on FreeBSD for PF_INET. 2014-04-17 21:23:19 +00:00
fhajny
dc42978d41 SunOS has rpc/xdr.h and builds xtcformat.so too. 2014-04-07 09:36:53 +00:00
fhajny
354d10fbe0 Update biology/bioperl to 1.6.923.
Way too many changes (0.7.0 was released in 2001!).

See changelog at:

https://github.com/bioperl/bioperl-live/blob/master/Changes
2014-02-20 14:44:16 +00:00
fhajny
c00a54ff57 Add p5-Bio-ASN1-EntrezGene 2014-02-20 11:44:51 +00:00
fhajny
2535650865 Import biology/p5-Bio-ASN1-EntrezGene.
Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez
Gene genome databases (http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene). It
parses an ASN.1-formatted Entrez Gene record and returns a data structure that
contains all data items from the gene record.
2014-02-20 11:43:56 +00:00
wiz
74706f73eb Add standard comment to not-ready-for-python line. 2014-02-17 14:32:48 +00:00
wiz
d562647396 Mark as not ready for python-3.x.
While here, slightly clean up Makefile and fix conflict with itself
by adding ${PYVERSSUFFIX} to pymol binary.
Bump PKGREVISION.
2014-02-17 14:32:28 +00:00
wiedi
1f326d79ad fix build on SunOS 2014-02-08 12:27:14 +00:00
wiz
aece887324 Convert to versioned_dependencies.mk for Pmw. 2014-01-18 19:56:36 +00:00
wiz
e03c03b6dc Recursive PKGREVISION bump for libgcrypt-1.6.0 shlib major bump. 2014-01-01 11:52:02 +00:00
jperkin
d35e64c22e Add socket libraries on SunOS. Patch from Sebastian Wiedenroth. 2013-12-10 14:18:05 +00:00
joerg
9755c6395e Fix extraction of rpath options from Fortran linker. 2013-11-29 12:53:26 +00:00
asau
4fe2717ab4 Update to chemtool 1.6.14
Fixes and enhancements in chemtool 1.6.14

- Updated configure script to support ARM64.
- Fixed potential crash during EPS output.
- Fixed detection of openbabel 2.3.x
2013-10-30 15:13:02 +00:00
ryoon
3fba1a52dd Recursive revbump from pango-1.36.0 2013-10-10 14:41:44 +00:00