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* New USES=eigenTobias C. Berner2018-01-021-5/+2
| | | | | | | | | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=457914
* - Update to 3.697Wen Heping2018-01-012-3/+4
| | | | Notes: svn path=/head/; revision=457755
* - Update to 5.16.0Wen Heping2018-01-013-4/+9
| | | | Notes: svn path=/head/; revision=457754
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1Joseph Mingrone2017-12-292-3/+4
| | | | Notes: svn path=/head/; revision=457516
* biology/iqtree: Update to version 1.6.1Joseph Mingrone2017-12-282-9/+8
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases Notes: svn path=/head/; revision=457467
* Disable the extra flag "-march=native" on arm to fix builds.Mark Linimon2017-12-271-3/+6
| | | | | | | | Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run Notes: svn path=/head/; revision=457351
* Update to 2.0.1Sunpoet Po-Chuan Hsieh2017-12-263-5/+31
| | | | | | | Changes: https://github.com/rvosa/bio-phylo/releases Notes: svn path=/head/; revision=457333
* biology/canu: Replace += with = for dependsJason W. Bacon2017-12-221-2/+2
| | | | | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13574 Notes: svn path=/head/; revision=456982
* - Fix build on 11+Dmitry Marakasov2017-12-222-4/+11
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=456976
* [new port] biology/canu: Single molecule sequence assemblerJason W. Bacon2017-12-226-0/+167
| | | | | | | | Approved by: jrm (mentor) or wen (mentor) Differential Revision: https://reviews.freebsd.org/D13574 Notes: svn path=/head/; revision=456950
* Try to bring some consistency to ports that have x86-specific pieces.Mark Linimon2017-12-212-12/+12
| | | | | | | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=456901
* Switch from swig 2.0 to swig 3.0Baptiste Daroussin2017-12-201-2/+4
| | | | Notes: svn path=/head/; revision=456845
* Mark more recently failing ports broken on aarch64.Mark Linimon2017-12-191-2/+3
| | | | | | | | | While here, pet portlint and reformat some other BROKEN statements. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=456719
* Back out previous commits by jbeich demand.Mark Linimon2017-12-182-10/+2
| | | | Notes: svn path=/head/; revision=456588
* Bah. Remove spare line from cut-and-paste.Mark Linimon2017-12-181-1/+0
| | | | Notes: svn path=/head/; revision=456579
* Attempt to fix build on non-x86 archs. Untested, but does no harmMark Linimon2017-12-182-2/+11
| | | | | | | | | on x86. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=456578
* biology/diamond: Update to version 0.9.14Joseph Mingrone2017-12-132-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14 Notes: svn path=/head/; revision=456220
* biology/seqtools: re-try on powerpc* after r449590Jan Beich2017-12-121-2/+0
| | | | Notes: svn path=/head/; revision=456096
* - Those ports fail to build with python3Antoine Brodin2017-12-111-1/+1
| | | | | | | - Add some explicit FLAVOR to dependencies where needed Notes: svn path=/head/; revision=456050
* Mark several ports newly broken on arm.Mark Linimon2017-12-112-3/+9
| | | | | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455927
* biology/py-biom-format: Add required dependency on math/py-pandas and doJoseph Mingrone2017-12-101-3/+7
| | | | | | | not install tests. Notes: svn path=/head/; revision=455879
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for ↵Jason W. Bacon2017-12-095-0/+47
| | | | | | | | | | adapter and quality trimming Approved by: jrm (mentor) Differential Revision: D13400 Notes: svn path=/head/; revision=455857
* These are also broken on aarch64 in the same way as armv6/7.Mark Linimon2017-12-091-0/+1
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455815
* Mark more ports broken that fail on both armv6 and armv7.Mark Linimon2017-12-091-0/+3
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455813
* Revert previous fat-fingered commit. These are the error messages fromMark Linimon2017-12-081-2/+2
| | | | | | | | | | benchmarks/libmicro. Pointy hat to: self Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455771
* Update errror message on armvX.Mark Linimon2017-12-081-2/+2
| | | | Notes: svn path=/head/; revision=455769
* biology/fasttree: update to version 2.1.10Jason W. Bacon2017-12-054-19/+45
| | | | | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D8187 Notes: svn path=/head/; revision=455562
* biology/py-macs2: Restrict to python 2.7.Jason W. Bacon2017-12-051-2/+2
| | | | | | | | | | Use ${PYNUMPY} per mat suggestion. Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13350 Notes: svn path=/head/; revision=455561
* Add a USES=python:env, that will not add a dependency on Python.Mathieu Arnold2017-12-042-4/+2
| | | | | | | | | | It has the same effect than setting PYTHON_NO_DEPENDS, but in a more compact way. Sponsored by: Absolight Notes: svn path=/head/; revision=455518
* Fix configure options for gnustep-makeDavid Chisnall2017-12-031-1/+1
| | | | | | | | | | 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. Notes: svn path=/head/; revision=455401
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation ↵Jason W. Bacon2017-12-024-0/+41
| | | | | | | | | | (ChIP) sequences Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13322 Notes: svn path=/head/; revision=455383
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ↵Jason W. Bacon2017-12-025-0/+91
| | | | | | | | | | data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13328 Notes: svn path=/head/; revision=455382
* Fix packaging with python3Antoine Brodin2017-12-012-14/+14
| | | | Notes: svn path=/head/; revision=455247
* [unbreak] biology/bwa: Remove old patch filesJason W. Bacon2017-12-013-37/+0
| | | | | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13314 Notes: svn path=/head/; revision=455246
* [new port] biology/fastqc: Quality control tool for high throughput sequence ↵Jason W. Bacon2017-11-305-0/+260
| | | | | | | | | | data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13304 Notes: svn path=/head/; revision=455236
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentJason W. Bacon2017-11-301-1/+0
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13303 Notes: svn path=/head/; revision=455235
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-309-17/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=455210
* For ports that are marked BROKEN on armv6, and also fail to build onMark Linimon2017-11-305-0/+5
| | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=455167
* biology/bowtie2: Upgrade to 2.3.3.1Jason W. Bacon2017-11-305-50/+19
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13300 Notes: svn path=/head/; revision=455161
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, poJason W. Bacon2017-11-295-0/+74
| | | | | | | | | ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294 Notes: svn path=/head/; revision=455154
* biology/bwa: Upgrade to 0.7.17Jason W. Bacon2017-11-282-5/+10
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13283 Notes: svn path=/head/; revision=455045
* biology/vcftools: Upgrade to latest release 0.1.15Jason W. Bacon2017-11-272-4/+4
| | | | | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13276 Notes: svn path=/head/; revision=455000
* - Switch to options helpersDmitry Marakasov2017-11-261-1/+5
| | | | Notes: svn path=/head/; revision=454906
* biology/diamond: Update to version 0.9.13Joseph Mingrone2017-11-172-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13 Notes: svn path=/head/; revision=454383
* - Update to 3.1b2Wen Heping2017-11-115-39/+69
| | | | | | | | | | | - Pass maintainership to submitter PR: 223561 Submitted by: mzaki@niid.go.jp Approved by: bacon4000@gmail.com(previous maintainer) Notes: svn path=/head/; revision=453972
* Fix the context of some patches so that they apply with stricter patch(1)Antoine Brodin2017-11-092-6/+6
| | | | | | | | PR: 223545 With hat: portmgr Notes: svn path=/head/; revision=453869
* biology/diamond: Update to version 0.9.12Joseph Mingrone2017-11-082-7/+5
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12 Notes: svn path=/head/; revision=453752
* Fix USE_GITHUB usage.Mathieu Arnold2017-11-062-5/+4
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=453620
* biology/py-pysam: Update to 0.13Yuri Victorovich2017-11-052-6/+8
| | | | | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D12967 Notes: svn path=/head/; revision=453556
* biology/diamond: Update to 0.9.11Joseph Mingrone2017-11-033-10/+14
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases Notes: svn path=/head/; revision=453387
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