Commit graph

2212 commits

Author SHA1 Message Date
Muhammad Moinur Rahman
1016ad8aac biology/seaview: Update version 4.6.2=>4.6.3
- Added pkg-plist to pet portlint

Relnotes:	http://doua.prabi.fr/software/seaview_data/CHANGES
2018-01-05 17:40:41 +00:00
Tobias C. Berner
51d04637cb New USES=eigen
Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702
2018-01-02 16:49:24 +00:00
Wen Heping
a049260311 - Update to 3.697 2018-01-01 08:40:22 +00:00
Wen Heping
8cc87f5485 - Update to 5.16.0 2018-01-01 08:24:53 +00:00
Joseph Mingrone
e84339cb2b biology/iqtree: Fix distinfo after upstream re-released v1.6.1 2017-12-29 17:14:07 +00:00
Joseph Mingrone
3baf04725e biology/iqtree: Update to version 1.6.1
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
2017-12-28 18:37:06 +00:00
Mark Linimon
f02e9b1855 Disable the extra flag "-march=native" on arm to fix builds.
Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
2017-12-27 07:36:05 +00:00
Sunpoet Po-Chuan Hsieh
de654cac5b Update to 2.0.1
Changes:	https://github.com/rvosa/bio-phylo/releases
2017-12-26 23:20:28 +00:00
Jason W. Bacon
b0cc388a5e biology/canu: Replace += with = for depends
Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D13574
2017-12-22 14:14:11 +00:00
Dmitry Marakasov
b945f4dc26 - Fix build on 11+
Approved by:	portmgr blanket
2017-12-22 12:27:14 +00:00
Jason W. Bacon
302f405a84 [new port] biology/canu: Single molecule sequence assembler
Approved by: jrm (mentor) or wen (mentor)
Differential Revision:  https://reviews.freebsd.org/D13574
2017-12-22 01:30:26 +00:00
Mark Linimon
bc6d0887a0 Try to bring some consistency to ports that have x86-specific pieces.
- in general, if we think that the code is not architecture-specific,
   and instead just enables x86 assembler by default, those should
   use BROKEN rather than IGNORE.  This will allow them to be attempted
   with TRYBROKEN.
 - spell i386 as x86.
 - spell asm as assembler.
 - pet portlint.

These changes should have no effect on tier-1 builds.

Approved by:	portmgr (tier-2 blanket)
2017-12-21 10:23:19 +00:00
Baptiste Daroussin
2e9911f602 Switch from swig 2.0 to swig 3.0 2017-12-20 19:34:11 +00:00
Mark Linimon
f1696c0036 Mark more recently failing ports broken on aarch64.
While here, pet portlint and reformat some other BROKEN statements.

Approved by:	portmgr (tier-2 blanket)
2017-12-19 14:41:29 +00:00
Mark Linimon
a3d16c9a04 Back out previous commits by jbeich demand. 2017-12-18 04:28:28 +00:00
Mark Linimon
c296605f05 Bah. Remove spare line from cut-and-paste. 2017-12-18 02:41:24 +00:00
Mark Linimon
91070ff927 Attempt to fix build on non-x86 archs. Untested, but does no harm
on x86.

Approved by:	portmgr (tier-2 blanket)
2017-12-18 02:32:47 +00:00
Joseph Mingrone
390c5f7f64 biology/diamond: Update to version 0.9.14
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
2017-12-13 16:31:53 +00:00
Jan Beich
7067236929 biology/seqtools: re-try on powerpc* after r449590 2017-12-12 03:38:56 +00:00
Antoine Brodin
1d00aa2b00 - Those ports fail to build with python3
- Add some explicit FLAVOR to dependencies where needed
2017-12-11 16:54:20 +00:00
Mark Linimon
5324a23092 Mark several ports newly broken on arm.
While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
2017-12-11 07:18:48 +00:00
Joseph Mingrone
1b5b3cea25 biology/py-biom-format: Add required dependency on math/py-pandas and do
not install tests.
2017-12-10 03:33:04 +00:00
Jason W. Bacon
7b14021ad6 [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming
Approved by: jrm (mentor)
Differential Revision:	D13400
2017-12-09 13:23:32 +00:00
Mark Linimon
8ae42417cc These are also broken on aarch64 in the same way as armv6/7.
Approved by:	portmgr (tier-2 blanket)
2017-12-09 01:39:19 +00:00
Mark Linimon
e8210b4758 Mark more ports broken that fail on both armv6 and armv7.
Approved by:	portmgr (tier-2 blanket)
2017-12-09 00:42:05 +00:00
Mark Linimon
da4494be28 Revert previous fat-fingered commit. These are the error messages from
benchmarks/libmicro.

Pointy hat to:	self
Approved by:	portmgr (tier-2 blanket)
2017-12-08 05:20:01 +00:00
Mark Linimon
1f026818ff Update errror message on armvX. 2017-12-08 05:05:11 +00:00
Jason W. Bacon
578a3edd2c biology/fasttree: update to version 2.1.10
Approved by:	jrm
Differential Revision:	https://reviews.freebsd.org/D8187
2017-12-05 03:03:38 +00:00
Jason W. Bacon
e1cf50b763 biology/py-macs2: Restrict to python 2.7.
Use ${PYNUMPY} per mat suggestion.

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D13350
2017-12-05 02:59:01 +00:00
Mathieu Arnold
6063af74e8 Add a USES=python:env, that will not add a dependency on Python.
It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.

Sponsored by:	Absolight
2017-12-04 15:27:29 +00:00
David Chisnall
f9197640d9 Fix configure options for gnustep-make
We were not setting the flag to select the GNUstep ABI, so were defaulting to
using the GCC-compatible version, which was likely to trigger a lot of subtle
bugs.  This was noticed when C++ exceptions thrown through Objective-C stack
frames caused segfaults.
2017-12-03 12:23:53 +00:00
Jason W. Bacon
9956039fdd [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13322
2017-12-02 20:46:28 +00:00
Jason W. Bacon
429caa13b5 [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13328
2017-12-02 20:44:28 +00:00
Antoine Brodin
b635ddf14b Fix packaging with python3 2017-12-01 06:18:17 +00:00
Jason W. Bacon
6658b5b134 [unbreak] biology/bwa: Remove old patch files
Approved by: jrm
Differential Revision:  https://reviews.freebsd.org/D13314
2017-12-01 02:42:54 +00:00
Jason W. Bacon
eb53d36e45 [new port] biology/fastqc: Quality control tool for high throughput sequence data
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13304
2017-11-30 22:54:29 +00:00
Jason W. Bacon
a64acd4f68 biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor comment
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13303
2017-11-30 22:11:04 +00:00
Mathieu Arnold
551be3c723 Convert Python ports to FLAVORS.
Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
  current python flavor.  It can be used in dependency lines when the
  port itself is not python flavored.  For example, deskutils/calibre.

  By default, all the flavors are generated.  To only generate flavors
  for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define
  BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf.

  In all the ports with Python dependencies, the *_DEPENDS entries MUST
  end with the flavor so that the framework knows which to build/use.
  This is done by appending '@${PY_FLAVOR}' after the origin (or
  @${FLAVOR} if in a Python module with Python flavors, as the content
  will be the same).  For example:

    RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}

PR:		223071
Reviewed by:	portmgr, python
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D12464
2017-11-30 15:50:30 +00:00
Mark Linimon
bf43557044 For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
2017-11-30 06:13:34 +00:00
Jason W. Bacon
82d79438ee biology/bowtie2: Upgrade to 2.3.3.1
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13300
2017-11-30 02:59:16 +00:00
Jason W. Bacon
0b07bc6a59 [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po
ly-A tails, etc
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13294
2017-11-29 22:17:43 +00:00
Jason W. Bacon
af6cd877c0 biology/bwa: Upgrade to 0.7.17
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13283
2017-11-28 15:21:01 +00:00
Jason W. Bacon
8391a24523 biology/vcftools: Upgrade to latest release 0.1.15
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13276
2017-11-27 23:05:40 +00:00
Dmitry Marakasov
0e54a3159c - Switch to options helpers 2017-11-26 09:00:21 +00:00
Joseph Mingrone
6ce3a81f62 biology/diamond: Update to version 0.9.13
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
2017-11-17 20:11:05 +00:00
Wen Heping
8c8dc2d005 - Update to 3.1b2
- Pass maintainership to submitter

PR:		223561
Submitted by:	mzaki@niid.go.jp
Approved by:	bacon4000@gmail.com(previous maintainer)
2017-11-11 12:51:52 +00:00
Antoine Brodin
48f5f5e82e Fix the context of some patches so that they apply with stricter patch(1)
PR:		223545
With hat:	portmgr
2017-11-09 20:45:04 +00:00
Joseph Mingrone
587f788379 biology/diamond: Update to version 0.9.12
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
2017-11-08 16:06:50 +00:00
Mathieu Arnold
6d9a5c87be Fix USE_GITHUB usage.
Sponsored by:	Absolight
2017-11-06 14:24:39 +00:00
Yuri Victorovich
e42e8b05d1 biology/py-pysam: Update to 0.13
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D12967
2017-11-05 19:12:28 +00:00