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* ${RM} already has -f.mat2016-10-213-3/+3
| | | | | | | PR: 213570 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight
* biology/diamond: update to version 0.8.24jrm2016-10-172-4/+4
| | | | | Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8268
* biology/diamond: update to version 0.8.23jrm2016-10-102-4/+4
| | | | | | | | | | | Upstream release notes: Added option to change the genetic code used for translation of query in blastx mode (option --query-gencode, see here for a list of possible values: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8202
* Mark BROKEN: unfetchable, size mismatchantoine2016-10-011-0/+1
| | | | Reported by: pkg-fallout
* biology/blat: Fix build with non-base SSLmarino2016-10-011-4/+4
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* Update PORTREVISION and dinstinfo due to upstream tarball changejrm2016-09-302-3/+4
| | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8083
* biology/paml: update to version 4.9c and various improvementsjrm2016-09-284-33/+48
| | | | | | | | | | | | | | | | | - Update to version 4.9c - Set LICENSE=GPLv3 - Use the variable PORTDOCS to automate the generation of the DOCS plist (as suggested by mat@). - Install dat/ examples/ and Technical/ directories as well as files in the root directory of the distribution tarball. - Fix broken permissions. - Delete Windows executables. - Build and install useful binaries not built by upstream's Makefile. - Update pkg-descr. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8040
* Update email address to jrm@FreeBSD.org for ports that I maintainjrm2016-09-243-5/+3
| | | | | | Reviewed by: mat, swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D7995
* - Update to 1.68wen2016-09-232-3/+4
| | | | | | PR: 212874 Submitted by: wen@(myself) Approved by: maintainer
* - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]pawel2016-09-156-28/+39
| | | | | | | - Fix spelling in pkg-descr PR: 212682 [1] Submitted by: Hannes Hauswedell (maintainer) [1]
* GOOGLE_CODE has gone away.mat2016-09-141-0/+2
| | | | | | | | | | - If a port has another upstream, remove GOOGLE_CODE - If a port only has GOOGLE_CODE mark it BROKEN Some ports have a local mirror configured but for security reasons, it is not considered upstream. Sponsored by: Absolight
* - Update to 0.8.22amdmi32016-09-142-4/+4
| | | | | PR: 212603 Submitted by: jrm@ftfl.ca (maintainer)
* biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)marino2016-09-111-3/+2
| | | | | | | All support platforms have libbz2.so in base, so this port will never pull in archivers/bzip2. Approved by: just-fix-it
* - Update to 1.72wen2016-09-112-4/+4
| | | | Changes: http://search.cpan.org/~cjfields/Bio-ASN1-EntrezGene-1.72/
* Most commonly used build systems support silent builds, when theyamdmi32016-09-101-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | hide actual commands executed and only show short summary line (like "CC foo.c"). CMake and ninja enable this by default, some autotools using ports do as well. This is unacceptable because we need complete build logs at any time, so we now switch to verbose build logs unconditionally. Note that this change deliberately affects ALL builds and not only package builds on cluster, because we need to be sure that user experiencing failure can always provide informative build log regardless of settings and without rerunning the build. Change summary: - Always do verbose builds for cmake, ninja and GNU configure (the latter includes check if --disable-silent-rules is actually supported by the configure script; there are isolated cases when it's not true) - Remove CMAKE_VERBOSE, NINJA_VERBOSE and CONFIGURE_ARGS=--disable-silent-rules from all ports which set them for this is no longer needed - Revert hacks for --disable-silent-rules support priorly committed to biology/ncbi-blast+ and net-p2p/mldonkey - no longer needed as well Submitted by: amdmi3 Reviewed by: mat Exp-run by: antoine Approved by: portmgr (mat, antoine) Differential Revision: D7534
* - Make configure script handle --disable-silent-rules gracefullyamdmi32016-09-061-1/+1
| | | | | PR: 212075 Approved by: portmgr blanket
* - Update to 0.8.20wen2016-09-062-4/+4
| | | | | PR: 212399 Submitted by: jrm@ftfl.ca(maintainer)
* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withtijl2016-09-062-4/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mk/Uses/linux.mk. - Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with USES+=linux:\1 in all ports. - Replace USE_LINUX_APPS with USE_LINUX in all ports. - Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some ports. - When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY are defined. - Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases that it is still necessary ports can run ${BRANDELF} from post-patch. - Remove AUTOMATIC_PLIST handling. Only one port used it. - Fix Linux MASTER_SITES. - Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with default versions framework. - bsd.port.mk: - Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX. - Put USE_LINUX_PREFIX handling after USES processing. - Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can give these variables a different default value. - When a package needs to run Linux ldconfig check before installation if Linux support is enabled. - emulators/linux_base-*: - Use USES=linux and remove duplication. - Remove files/lp. FreeBSD or CUPS lp(1) should work. - Remove files/yp.conf. No longer seems to be used. - Remove pkg-deinstall and move pkg-install into pkg-plist. - Update pkg-descr and pkg-message. - Fix handling of ldconfig cache in pkg-plist. - devel/fb-adb: Use a Linux shell to run a Linux script but patch the script to use FreeBSD mkdir so mkdir -p $path creates $path and not /compat/linux/$path. PR: 211645 Exp-run by: antoine Approved by: portmgr (antoine)
* biology/molden: 5.4 -> 5.7pi2016-08-262-6/+4
| | | | | | | | | | - Adds editable text fields that are longer than the visible string and introduces a new way of selecting a range of amino acids. - introduces interfaces to the open source packages openbabel and pharmer. Openbabel is used to create 2D images of the molecules in a .sdf file. It is also used to do 2D fingerprint searching. Pharmer is used to pharmacophore (3D) searching against indexed databases of .sdf files.
* Update to version 0.8.19pawel2016-08-262-4/+4
| | | | | PR: 212145 Submitted by: Joseph Mingrone (maintainer)
* - Mark BROKEN: does not fetch (distfile was removed from ftp)amdmi32016-08-221-0/+2
| | | | Approved by: portmgr blanket
* biology/bedtools is not jobs safemarino2016-08-221-0/+2
| | | | | The version.o target tries to use version_git.h before that header is created.
* - Switch to options helpersamdmi32016-08-183-16/+11
| | | | | - Regenerate patches with `make makepatch` - Mark WXGTK option broken: does not build: src/convErr/gc_errhandling.cpp:75:12: error: cannot initialize return object of type 'const char *' with an rvalue of type 'const wxChar *' (aka 'const wchar_t *')
* Update biology/diamond to 0.8.18.brd2016-08-152-4/+4
| | | | | | PR: 211845 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer) Approved by: bdrewery (implicit)
* - Update to 1.9 [1]wen2016-08-082-10/+8
| | | | | | | | | | | - Moved to github [1] - Depend on newer sqlalchemy10 [1] - Update pkg-descr and WWW [1] - Limit python to -2.7 [2] - Reset maintainer to python@ for better maintain PR: 211621 Submitted by: pi@ [1], koobs@ [2]
* Update to version 0.8.17pawel2016-08-062-5/+5
| | | | | PR: 211582 Submitted by: Joseph Mingrone (maintainer)
* biology/seqtools: 4.42.1 -> 4.43.0pi2016-07-313-17/+227
| | | | | | ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html - Mark broken on 9.x: Fails to build due to C++ std issues
* Update to upstream release 0.8.16riggs2016-07-252-4/+4
| | | | | PR: 211335 Submitted by: jrm@ftfl.ca (maintainer)
* Cleanup $() variables in ports Makefiles.mat2016-07-201-1/+1
| | | | | | | Mostly replace with ${}, but sometime, replace with $$() because it is what was intended in the first place. (I think.) Sponsored by: Absolight
* - update libgd to 2.2.2dinoex2016-07-201-1/+1
| | | | | | | | | | | - new MASTER_SITES - add security patch PR: 210913 Submitted by: Piotr Kubaj MFH: 2016Q3 Security: CVE-2015-8874 Security: CVE-2016-3074 Security: http://www.openwall.com/lists/oss-security/2016/07/12/4
* When there is a do-install target, do not use a post-install target, domat2016-07-193-4/+5
| | | | | | | | | | | | everything at once. Sometime, rename post-install into a options helper target. I did not fix ports that were such a mess that I could not figure out what they really wanted to do. I also did not change ports that had some version of an auto-plist code in post-install, for the same reason. With hat: portmgr Sponsored by: Absolight
* Trim excess tabs, no-op changepawel2016-07-151-13/+13
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* Update to version 0.8.14pawel2016-07-152-4/+4
| | | | | PR: 211078 Submitted by: Joseph Mingrone (maintainer)
* - Update to 0.8.11amdmi32016-07-072-5/+5
| | | | | PR: 210877 Submitted by: jrm@ftfl.ca (maintainer)
* Remove expired ports without open PRs:rene2016-07-057-161/+0
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* - LICENSEamdmi32016-07-022-10/+22
| | | | | - Optionalize NLS - Switch to options helpers
* biology/diamond: update 0.8.6 -> 0.8.9junovitch2016-06-302-4/+4
| | | | | PR: 210710 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
* - Add missing dependency, fixing buildamdmi32016-06-241-1/+5
| | | | - Switch to options helpers
* - Switch to options helpersamdmi32016-06-212-7/+11
| | | | - Regenerate patches with `make makepatch`
* biology/diamond: update to 0.8.6rm2016-06-182-4/+4
| | | | | PR: 210345 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
* - Fix run-time dependency issuesolivierd2016-06-111-2/+13
| | | | | | | - Bump PORTREVISION PR: 209767 Submitted by: Joseph Mingrone (maintainer)
* biology/seaview: Update version 4.5.4.8=>4.6bofh2016-06-102-7/+4
| | | | - UNBREAK
* Update to 0.8.5matthew2016-06-093-34/+18
| | | | | PR: 209611 Submitted by: jrm@ftfl.ca (maintainer)
* - Update to 1.35wen2016-06-082-3/+4
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* Remove unneeded usage of:mat2016-06-061-2/+1
| | | | | | | | - MASTER_SITE_SUBDIR - ${MASTER_SITES_FOO} - :DEFAULT (and use a default when appropriate) Sponsored by: Absolight
* Deprecate ports broken for more than 6 monthsantoine2016-06-042-0/+4
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* - Do install cmake and pkgconfig modulesamdmi32016-05-282-3/+8
| | | | | | | - While here, switch to options helpers PR: 209710 Submitted by: h2+fbsdports@fsfe.org (maintainer)
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1pi2016-05-278-20/+23
| | | | | | | | Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer)
* Remove useless WRKSRC definitions.mat2016-05-251-2/+0
| | | | | | While there, correct DEV_WARNINGS when they occur. Sponsored by: Absolight
* - Fix trailing whitespace in pkg-messagesamdmi32016-05-196-12/+12
| | | | Approved by: portmgr blanket
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*amdmi32016-05-1921-36/+36
| | | | Approved by: portmgr blanket
* Fix DEPENDSantoine2016-05-191-2/+2
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* - Convert to USES=mysqlamdmi32016-05-171-8/+4
| | | | - Cosmetic fixes
* - Update to 4.9aamdmi32016-05-172-4/+7
| | | | | | | - While here, simplify WRKSRC and use options helpers PR: 209535 Submitted by: jrm@ftfl.ca (maintainer)
* biology/bowtie2: 2.2.7 -> 2.2.8pi2016-05-142-3/+3
| | | | | | | | | - Various website updates - Fixed the bowtie2-build issue that made TBB compilation fail PR: 208943 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: Jason Bacon <bacon4000@gmail.com> (maintainer)
* Prevent collision with getline(3)bapt2016-05-141-0/+300
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* Prevent collision with getline(3)bapt2016-05-141-0/+291
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* Prevent collision with getline(3)bapt2016-05-124-6/+27
| | | | While here regen patches
* biology/seqan: update 1.3.1 -> 2.1.1junovitch2016-05-1012-1915/+3706
| | | | | | | | biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
* New port: biology/seqan-appsjunovitch2016-05-105-0/+220
| | | | | | | | | | | | | | | | | SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged seperately and the library can be found at biology/seqan. WWW: http://www.seqan.de/ PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
* Add final slash in WWW entryolivierd2016-05-101-1/+1
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* The BIOM file format (canonically pronounced biome) is designed to be aolivierd2016-05-104-0/+48
| | | | | | | | | | | | | | | | | | | | | | | | general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. WWW: http://biom-format.org/ PR: 209193 Submitted by: Joseph Mingrone
* During the exp-run in bug 208158, it was found that biology/ugene givesdim2016-05-084-0/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | errors with libc++ 3.8.0: In file included from src/QScoreAdapter.cpp:1: In file included from src/QScoreAdapter.h:4: In file included from ../../include/U2Core/MAlignment.h:1: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25: In file included from /usr/local/include/qt5/QtCore/QString:1: In file included from /usr/local/include/qt5/QtCore/qstring.h:41: In file included from /usr/local/include/qt5/QtCore/qchar.h:37: In file included from /usr/local/include/qt5/QtCore/qglobal.h:39: /usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found #include_next <stddef.h> ^ This is because the port tries to add /usr/include as a system include directory, using -isystem, and this screws up the order of include directories. Fix it by patching up a number of .pri files to avoid using the -isystem flag. Approved by: h2+fbsdports@fsfe.org (maintainer) PR: 209366 MFH: 2016Q2
* DNA query sequences against a protein reference database (BLASTP and BLASTXwen2016-05-065-0/+71
| | | | | | | | | | | alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca
* - Update to 1.14.8danilo2016-05-013-4/+4
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* biology/seqtools: 4.41.1 -> 4.42.1pi2016-04-232-5/+5
| | | | | | | - fixes build on 9.x - Added a feedback box to show the read depth at the selected coord. Hover over this box to see the specific base support (i.e. the number of A/C/G/Ts).
* many ports: mark broken on powerpc64swills2016-04-221-0/+2
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* - Switch to options helpersamdmi32016-04-173-16/+17
| | | | | - Regenerate patches with `make makepatch` - Simplify plist
* - Update to 1.66wen2016-04-172-4/+3
| | | | | | PR: 208825 Submitted by: wen@ Approved by: maintainer
* - Switch to options helpersamdmi32016-04-161-3/+8
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* Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:mi2016-04-163-4/+5
| | | | | | https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78 Notified by: portscout
* Update to version 1.22.0, which now unfortunately requires Qt 5.x. Alsodanfe2016-04-149-36/+204
| | | | | | | since around v1.18.0, UGENE is using Google's Breakpad library for crash reporting, which is very system-specific and does not support FreeBSD at the moment. Due to lack of resources and interest in porting it, simply disable crash reporting code for the time being.
* - Add LICENSEamdmi32016-04-101-1/+8
| | | | - Switch to options helpers
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.mat2016-04-0138-148/+148
| | | | | With hat: portmgr Sponsored by: Absolight
* - Update to 1.5.0amdmi32016-04-013-23/+11
| | | | | | PR: 208351 Submitted by: wen@FreeBSD.org Approved by: mauricio@arareko.net (maintainer)
* - Use more appropriate BROKEN instead of IGNOREamdmi32016-03-301-4/+2
| | | | | | PR: 208367 Submitted by: bacon4000@gmail.com (maintainer) Suggested by: rakuco
* - Update to 5.12.0wen2016-03-273-5/+7
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* - Clarify LICENSEamdmi32016-03-241-4/+3
| | | | | | | | - Add LICENSE_FILE - Remove USES=tar:bzip2 (incorrect and no-op with USE_GITHUB) - Drop unneeded (and incorrect anyway) PKG_CONFIG_PATH Approved by: portmgr blanket
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.amdmi32016-03-246-0/+146
| | | | | | | | | | | | A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com
* New port: biology/bowtie2.rakuco2016-03-236-0/+134
| | | | | | | | | | | | | | | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. This is Bowtie version 2, which will need to coexists with Bowtie 1 for the foreseeable future. Both are required by certain genomics pipelines, in some cases (e.g. Trinity) by the same pipeline. WWW: https://github.com/BenLangmead/bowtie2 PR: 207908 Submitted by: Jason Bacon <bacon4000@gmail.com>
* New port: biology/slclust.rakuco2016-03-236-0/+85
| | | | | | | | | | | Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. WWW: http://sourceforge.net/projects/slclust/ PR: 207997 Submitted by: Jason Bacon <bacon4000@gmail.com>
* Trimmomatic performs a variety of useful trimming tasks for illuminawen2016-03-175-0/+41
| | | | | | | | | NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com
* New port: biology/p5-transdecoderpi2016-03-175-0/+88
| | | | | | | | | | | | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. WWW: http://transdecoder.github.io/ PR: 207993 Submitted by: Jason Bacon <bacon4000@gmail.com>
* biology/seqtools: 4.40.0 -> 4.41.1pi2016-03-153-4/+6
| | | | - mostly internal changes, some build fixes
* Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.mat2016-03-081-2/+2
| | | | | | | | | | | | Fix distinfo for the offending ports. lang/yorick's tag was moved, and the added patch was no longer needed. PR: 207644 Submitted by: mat Exp-run by by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D4268
* New port: biology/bowtie.rakuco2016-03-056-0/+194
| | | | | | | | | | | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com>
* New port: biology/vcftools.rakuco2016-02-275-0/+59
| | | | | | | | | | A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. WWW: https://github.com/vcftools/vcftools PR: 206926 Submitted by: Jason Bacon <bacon4000@gmail.com>
* - Update to 3.2.0wen2016-02-263-34/+62
| | | | | | | - Update pkg-descr PR: 205890 Submitted by: tkato432@yahoo.com
* - Update to 1.14.7danilo2016-02-212-3/+3
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* - Update to 1.34wen2016-02-122-3/+3
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* biology/seqtools: 4.39.3 -> 4.40.0pi2016-02-062-3/+3
| | | | | | | - Blixem can now accept a 'command' tag in a gff line for a region feature. The given command should return gff and will be run by blixem on the given region. - Blixem now supports fetching sequence data over https.
* biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGSmarino2016-02-021-0/+2
| | | | | | Also link with libncurses, not libtermcap approved by: infrastructure blanket
* biology/samtools: document ncurses requirement (USES+=ncurses)marino2016-02-021-1/+1
| | | | approved by: infrastructure blanket
* biology/molden: updated distfile, take maintainerpi2016-01-212-4/+4
| | | | | | - upstream distfile is moving target with same version number Submitted by: antoine
* Mark BROKEN: checksum and size mismatchantoine2016-01-211-0/+1
| | | | Reported by: pkg-fallout
* The bedtools utilities are a suite of tools for performing a wide range ofwen2016-01-196-0/+135
| | | | | | | | | | | | | | | | | genomics analysis tasks. The most widely-used of these tools enable genome arithmetic, i.e., set theory on the genome. For example, with bedtools one can intersect, merge, count, complement, and shuffle genomic intervals from multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts. WWW: http://bedtools.readthedocs.org/ PR: 204536 Submitted by: scottcheloha@gmail.com
* biology/molden: 5.0.7 -> 5.4pi2016-01-195-192/+799
| | | | | | | | | | | | | | Changes: - Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally. - Pdb files can now be clipped. - Fixes missing residues. Introduces an alternative way of generating rotamers, without using z-matrices. This potentially a faster algorithm. - Supports Movie making through avconv/ffmpeg. - calculates the Electron Localization Function (ELF). - Updated code of ambfor/ambmd to speed up optimisations/MD of proteins solvated in water (Jan, 2014). PR: 204341
* mark ports that don't work with Ruby 2.3swills2016-01-171-0/+1
| | | | PR: 205774
* Convert LICENSE= "GPLxx # or later" to "GPLxx+"amdmi32016-01-134-4/+4
| | | | Approved by: portmgr blanket
* Add Public Domain support to ports license framework. You can now useamdmi32016-01-121-3/+1
| | | | | | | | | | | | | LICENSE= PD Note that although Public Domain is not technically a license, it's handled in the same way as licenses here, which is a common practice (Arch, Gentoo, Fedora, Debian, even FOSSology do the same). Convert all ports which redefine Public Domain LICENSE to LICENSE=PD. Approved by: portmgr (bapt) Differential Revision: D4149
* Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRSpawel2016-01-101-2/+0
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* biology/crux is not jobs safemarino2015-12-311-0/+2
| | | | | This cython-based port has failed on me a couple of times in a bulk build. I'm not sure what the actual problem is but the issue is itermittent.
* biology/htslib: Replace FreeBSD-specific fix with a generic onemarino2015-12-291-5/+4
| | | | | | | This port will not build if ENOTRECOVERABLE is not defined, period. It's not necessary to check OPSYS and version, just apply the fallback definition if it's not defined. This unbreaks DragonFly after last commit.
* Cleanup GH_* and variables order.mat2015-12-293-3/+1
| | | | Sponsored by: Absolight
* biology/consed: undeprecate, it presumably builds fine but it is restricted.rene2015-12-261-5/+1
| | | | Add a note to ports/LEGAL
* - Update to 7.266wen2015-12-255-42/+133
| | | | | PR: 205558 Submitted by: cartwright@asu.edu(maintainer)
* biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3junovitch2015-12-2527-173/+930
| | | | | | | | | | | | | - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require version 1.3 of htslib. - Add CURL option to htslib - Add TEST_TARGET with perl and bash dependencies for testing - Tidy up spacing and pkg-message's PR: 205524 PR: 205525 PR: 205526 Submitted by: cartwright@asu.edu (maintainer)
* mark some of the ports that don't build on powerpc64 for meswills2015-12-144-0/+7
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* - Update maintainer mail addressmiwi2015-12-1112-23/+22
| | | | | | | | | - Update/Remove MASTER_SITE PR: 204755 Submitted by: jwbacon@tds.net (maintainer) Approved by: mat (mentor) Differential Revision: D4493
* - Update to 1.32wen2015-12-113-6/+8
| | | | | - Add LICENSE - Pet portlint
* biology/seqtools: 4.39.2 -> 4.39.3pi2015-12-052-3/+3
| | | | | | | - Blixem Further improve the display of features in the detail view when they have transparent fill, making sure that they have a visible border.
* biology/seqtools: 4.39.1 -> 4.39.2pi2015-12-022-3/+3
| | | | | | - Blixem: Improve the display of features in the detail view when they have transparent fill.
* - Mark BROKEN: checksum mismatch:amdmi32015-11-291-0/+2
| | | | fetch: http://www.platonsoft.nl/spek/xraysoft/unix/platon.tar.gz: size mismatch: expected 12080181, actual 12080357
* Remove expired ports:rene2015-11-2915-933/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2015-11-26 audio/pecl-id3: Broken for more than 6 months 2015-11-26 dns/geta: Broken for more than 6 months 2015-11-26 finance/openerp-web: Broken for more than 6 months 2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream 2015-11-26 chinese/kon2: Depends on expiring chinese/cce 2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi 2015-11-26 archivers/wzip: Broken for more than 6 months 2015-11-26 databases/sybtcl: Broken for more than 6 months 2015-11-26 biology/povchem: Broken for more than 6 months 2015-11-26 audio/btc: Broken for more than 6 months 2015-11-26 astro/wmglobe: Broken for more than 6 months 2015-11-26 graphics/pyro: Broken for more than 6 months 2015-11-26 graphics/jpeg2ps: Broken for more than 6 months 2015-11-26 chinese/gugod-clean: Broken for more than 6 months 2015-11-26 comms/bforce: Broken for more than 6 months 2015-11-26 cad/geda-docs: Broken for more than 6 months 2015-11-26 chinese/cwtexttf: Broken for more than 6 months 2015-11-26 comms/zmtx-zmrx: Broken for more than 6 months 2015-11-26 astro/sky2000: Broken for more than 6 months 2015-11-26 deskutils/libopensync-plugin-file: Broken for more than 6 months 2015-11-26 databases/sqlite-ext-mobigroup: Broken for more than 6 months 2015-11-26 chinese/bg5ps: Broken for more than 6 months 2015-11-26 deskutils/x-tile: Broken for more than 6 months 2015-11-26 graphics/pure-gl: Broken for more than 6 months 2015-11-26 audio/dvda-author: Broken for more than 6 months 2015-11-26 chinese/oxim: Broken for more than 6 months 2015-11-26 editors/spe: Broken for more than 6 months 2015-11-26 audio/mpdscribble: Broken for more than 6 months 2015-11-26 cad/geda-symcheck: Broken for more than 6 months 2015-11-26 audio/linux-fmodapi: Broken for more than 6 months 2015-11-26 audio/pure-audio: Broken for more than 6 months 2015-11-26 editors/bpatch: Broken for more than 6 months 2015-11-26 benchmarks/geekbench: Broken for more than 6 months 2015-11-26 graphics/icoconvert: Broken for more than 6 months 2015-11-26 cad/geda-utils: Broken for more than 6 months 2015-11-26 deskutils/tomboy-plugin-wordcount: Broken for more than 6 months 2015-11-26 graphics/sketch: Broken for more than 6 months 2015-11-26 ftp/spegla: Broken for more than 6 months 2015-11-26 graphics/clutter-box2d: Broken for more than 6 months 2015-11-26 audio/scmpc: Broken for more than 6 months 2015-11-26 ftp/gnusget: Broken for more than 6 months 2015-11-26 comms/gpsk31: Broken for more than 6 months 2015-11-26 cad/geda-gschem: Broken for more than 6 months 2015-11-26 audio/ampache: Broken for more than 6 months 2015-11-26 cad/slffea: Broken for more than 6 months 2015-11-26 audio/cripple: Broken for more than 6 months 2015-11-26 cad/geda-gattrib: Broken for more than 6 months 2015-11-26 cad/findhier: Broken for more than 6 months 2015-11-26 biology/njplot: Broken for more than 6 months 2015-11-26 audio/wmmp: Broken for more than 6 months 2015-11-26 x11/avant-window-navigator: Broken for more than 6 months 2015-11-26 cad/geda-netlist: Broken for more than 6 months 2015-11-26 deskutils/libopensync-plugin-sunbird: Broken for more than 6 months 2015-11-26 biology/ortep3: Broken for more than 6 months 2015-11-26 astro/aa: Broken for more than 6 months 2015-11-26 french/belote: Broken for more than 6 months 2015-11-26 converters/p5-String-SetUTF8: Broken for more than 6 months 2015-11-26 cad/geda-examples: Broken for more than 6 months 2015-11-26 editors/yasnippet: Broken for more than 6 months 2015-11-26 audio/musica: Broken for more than 6 months 2015-11-26 graphics/rubyphoto: Broken for more than 6 months 2015-11-26 german/bsdpaste: Broken for more than 6 months 2015-11-26 audio/amrcoder: Broken for more than 6 months 2015-11-26 sysutils/bashburn: Broken for more than 6 months 2015-11-26 editors/e93: Broken for more than 6 months 2015-11-26 audio/tepsonic: Broken for more than 6 months 2015-11-26 astro/ephem: Broken for more than 6 months 2015-11-26 chinese/cce: Broken for more than 6 months 2015-11-26 graphics/qcread: Broken for more than 6 months 2015-11-26 databases/py-sqlkit: Broken for more than 6 months 2015-11-26 databases/usogres: Broken for more than 6 months 2015-11-26 cad/libgeda: Broken for more than 6 months 2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months 2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months 2015-11-26 deskutils/mrundlg: Broken for more than 6 months 2015-11-26 databases/erlang-mysql: Broken for more than 6 months 2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months 2015-11-26 deskutils/akamaru: Broken for more than 6 months 2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months 2015-11-26 astro/dgpsip: Broken for more than 6 months 2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months 2015-11-26 audio/cymbaline: Broken for more than 6 months 2015-11-26 french/dico: Broken for more than 6 months 2015-11-26 comms/qpage: Broken for more than 6 months 2015-11-26 audio/sonice: Broken for more than 6 months 2015-11-26 cad/geda-symbols: Broken for more than 6 months 2015-11-26 databases/java-mybatis: Broken for more than 6 months 2015-11-26 databases/openbase-jdbc: Broken for more than 6 months 2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25 2015-11-28 www/R-cran-Rpad: Unmaintained upstream
* biology/platon: fix fetchingrm2015-11-203-6/+4
| | | | | | | | | | Add working mirror. Also update file size in distinfo - checksum is not changed and I dunno why. But with old file size it warns that expected size was different. PR: 204491 Submitted by: Walter Schwarzenfeld <w.litter@aon.at>
* - Switch to options helpersamdmi32015-11-191-1/+1
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* biology/seqtools: Fix distinfo, WWWpi2015-11-182-3/+3
| | | | | | - Side effect of the seqtools automated build system Submitted by: pkg-fallout
* biology/seqtools: 4.39.0 -> 4.39.1pi2015-11-142-3/+3
| | | | | - Fix a bug in Belvu where the display was being initialised in command-line-only modes.
* - Update to 1.14.6danilo2015-11-103-4/+4
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* Mark a few ports BROKEN: unfetchableantoine2015-11-091-0/+2
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* biology/seqtools: 4.36 -> 4.39.0pi2015-11-092-3/+3
| | | | | | | | | | | | | | - Blixem o There is now an optional setting to highlight "maybe-canonical" splice sites in Blixem. This can be used to help identify problems where the strand is incorrect in the input data - it highlights splice sites in a different colour if they would be canonical were they on the other strand. o Fixed a bug with colinearity lines when an alignment's cigar string contains introns. o There are now separate feedback boxes for the selected sequence name coordinates. Hover over each box to see a tooltip describing its contents.
* - Update to 1.14.5danilo2015-11-063-4/+4
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* Fix ports that confused the meaning of WRKDIR and WRKSRC.mat2015-11-051-5/+5
| | | | | | | | PR: 204056 Submitted by: mat Reviewed by: bapt Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D2735
* biology/seaview: Broken, Does not fetch (checksum mismatch)marino2015-11-021-0/+2
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* - Update to 2015.09.21madpilot2015-10-285-25/+60
| | | | | | | | | | | | - Add License - Add SIMD option disabled by default to avoid creating official packags with CPU specific optimizations - Add pkg-message explaining how to get an optimized binary - Assign maintainership to submitter PR: 203334 Submitted by: jwbacon at tds.net Approved by: Maintainer timeout
* Deprecate ports broken for more than 6 monthsantoine2015-10-264-0/+8
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* biology/seaview: Update version 4.5.4.7=>4.5.4.8bofh2015-10-202-3/+3
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* - Update to 36.3.8danilo2015-10-162-4/+4
| | | | | | | - Pass maintainership to submitter PR: 203817 Submitted by: Wendell Borges <wendell@bsd.com.br>
* - Add LICENSE_FILEamdmi32015-10-151-1/+2
| | | | - Switch to options helpers
* - Pet portlintamdmi32015-10-151-4/+5
| | | | | - Add LICENSE - Drop unneeded WX_UNICODE
* - Fix typosunpoet2015-10-111-1/+1
| | | | Approved by: portmgr (blanket)
* - Update to 1.14.4danilo2015-10-073-4/+4
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* - Update to 1.14.3danilo2015-10-023-4/+4
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* biology/seaview: Update version 4.5.4.6=>4.5.4.7bofh2015-10-012-4/+3
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* biology/grappa: define license (GPLv2)rm2015-09-261-0/+2
| | | | | | | | As per the web site, the license for GRAPPA is GPLv2 https://www.cs.unm.edu/~moret/GRAPPA/ PR: 202426 Submitted by: George <george@nycbug.org>
* BWA is a program for aligning sequencing reads against a large referencerm2015-09-268-0/+84
| | | | | | | | | | genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. WWW: http://sourceforge.net/projects/bio-bwa/ PR: 203158 Submitted by: Jason Bacon <jwbacon@tds.net>
* Fast indexing and retrieval of FASTA records from flat file data bases.rm2015-09-265-0/+85
| | | | | | | WWW: http://sourceforge.net/projects/cdbfasta/ PR: 203233 Submitted by: Jason Bacon <jwbacon@tds.net>
* Simple and quick FastQ and FastA tool for file reading and conversion.rm2015-09-264-0/+39
| | | | | | | WWW: https://github.com/fstrozzi/Fastool PR: 203293 Submitted by: Jason Bacon <jwbacon@tds.net>
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromrm2015-09-264-0/+41
| | | | | | | | | | alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. WWW: http://www.microbesonline.org/fasttree/ PR: 203295 Submitted by: Jason Bacon <jwbacon@tds.net>
* The FASTX-Toolkit is a collection of command line tools for Short-Readsrm2015-09-265-0/+57
| | | | | | | | | FASTA/FASTQ files preprocessing. WWW: http://hannonlab.cshl.edu/fastx_toolkit/ PR: 203318 Submitted by: Jason Bacon <jwbacon@tds.net>
* Gordon's text utilities.rm2015-09-265-0/+50
| | | | | | | WWW: https://github.com/agordon/libgtextutils PR: 203309 Submitted by: Jason Bacon <jwbacon@tds.net>
* Typos, whitespace and capitalization fixes (A-F).olgeni2015-09-211-1/+1
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* - Use compiler:openmp instead of gccwen2015-09-191-4/+1
| | | | | | - Minor cleanup Reported by: danfe@
* CD-HIT is a very widely used program for clustering and comparing protein orwen2015-09-195-0/+81
| | | | | | | | | nucleotide sequences. WWW: http://weizhong-lab.ucsd.edu/cd-hit/ PR: 203183 Submitted by: jwbacon@tds.net
* Make all GNUstep ports install into the System domain so that the Local ↵theraven2015-09-192-66/+66
| | | | | | | | | | | domain is available for stuff built from source. Some ports were already installing in the System domain, for these just remove the Makefile lines explicitly specifying the install domain. The rest are installed in the Local domain, remove any overrides, update their pkg-plists and any explicit paths in the Makefiles and then bump port revision. Approved by: bapt (mentor) Differential Revision: https://reviews.freebsd.org/D2977
* - Update to 1.14.2danilo2015-09-173-4/+5
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* Remove ansi version fo wxGTK 2.8 and only keep the unicode versionbapt2015-09-172-1/+2
| | | | | | | | All applications in the ports tree works correctly with unicode version of wxGTK Newer version of wxGTK are unicode only (3.0+) Note that now WX_UNICODE macro is noop
* biology/seaview: Update version 4.5.4.4=>4.5.4.6bofh2015-09-152-5/+5
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* Make it so that the default Perl is always called perl5.mat2015-09-145-72/+72
| | | | | | | | | | | | | | | | - Move Perl's man1 files along with its man3 files. - Move where Perl installs its modules man1 pages. - Convert the ports installing man1 pages. - Make different Perl versions installable at the same time. Though you should note that only the default version can be used to install Perl modules, and the non default Perl versions cannot use the modules installed via ports if they contain .so as they are installed in a version specific directory. Reviewed by: bapt (the Mk bits) Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3542
* Enfoce unicode version of wxGTKbapt2015-09-141-0/+1
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* - Update to 1.14.1danilo2015-09-143-5/+5
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* - Add LICENSEsunpoet2015-09-042-8/+8
| | | | | | | | | - Add NO_ARCH - Use BROKEN_RUBY22 - While I'm here, use single space after WWW: Approved by: portmgr (blanket) With hat: ruby
* - Unbreak on PowerPC by using atomicops implementation for Linux and GCCdanfe2015-09-022-12/+40
| | | | | | | __sync_* functions family - Remove BROKEN_ia64: it never had been first-class architecture, killed officially in -CURRENT for a while now - Sanitize installation commands and sort the knobs while I am here
* - Do not falsely advertise that PowerPC build runs out of space and failsdanfe2015-09-021-11/+5
| | | | - Remove redundant PKGMESSAGE assignment and sanitize symlinks while here
* Unbreak the build on PowerPC (at least) by always using va_copy() macro fordanfe2015-09-022-20/+7
| | | | copying variable argument lists, not just on AMD64.
* Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":danfe2015-09-022-2/+20
| | | | | | | | configure script was passing `-faltivec' to the compiler, while this flag is non-standard and only supported on Mac OS X/Darwin systems. Also replace Apple-specific Altivec detection with querying the "hw.altivec" sysctl instead.
* - Switch to options helpersamdmi32015-09-021-6/+2
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* Switch to USES=iconv:build.rakuco2015-08-251-1/+2
| | | | | The port does not use iconv on its own, the only dependency comes via libxml2, which has one header that includes iconv.h.
* Fix previous commit.mat2015-08-191-1/+0
| | | | | Pointy hat to: mat Sponsored by: Absolight
* Convert ports to use the options helpers in categories [abc]*, and minor fixes.mat2015-08-197-41/+17
| | | | | Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3412?
* biology/ugene: qt4-linguist -> qt4-linguisttoolspgollucci2015-08-191-2/+3
| | | | | | | | - add USES=desktop-file-utils PR: 202138 Submitted by: s3erios@gmail.com Approved by: h2+fbsdports@fsfe.org
* Remove UNIQUENAME and LATEST_LINK.mat2015-08-171-2/+0
| | | | | | | | | | | | | | | | | UNIQUENAME was never unique, it was only used by USE_LDCONFIG and now, we won't have conflicts there. Use PKGBASE instead of LATEST_LINK in PKGLATESTFILE, the *only* consumer is pkg-devel, and it works just fine without LATEST_LINK as pkg-devel has the correct PKGNAME anyway. Now that UNIQUENAME is gone, OPTIONSFILE is too. (it's been called OPTIONS_FILE now.) Reviewed by: antoine, bapt Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3336
* biology/seqtools: 4.35 -> 4.36pi2015-08-082-3/+3
| | | | Minor under-the-hood changes
* Fix build on mips by properly respecting compiler and flagsamdmi32015-08-052-9/+20
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* Update to 1.65.mat2015-08-052-4/+4
| | | | | | | PR: 201888 Submitted by: brueffer Approved by: maintainer Sponsored by: Absolight
* Unbreakantoine2015-07-291-1/+1
| | | | Reported by: pkg-fallout
* - Fix four cases of an obvious typo: LICENSE_FILES -> LICENSE_FILEdanfe2015-07-251-2/+2
| | | | | | - While here: move knobs to their expected location, remove useless check for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize Makefile headers
* - Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)danfe2015-07-152-16/+11
| | | | - Remove no longer required local source code tweaks (picked up upstream)
* - Update to 1.14.0danilo2015-07-133-4/+5
| | | | - Use install-strip
* biology/seqtools: 4.34.1 -> 4.35pi2015-07-072-5/+5
| | | | | | | - Blixem bug fix in sorting features, RT 473624 - Compilation of the seqtools in parallel, RT 467905 - Fix bug with sorting by similarity/identity to first sequence (RT:473624) - Fix an error compiling with multiple threads (RT:467905)
* After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary,adamw2015-06-291-5/+2
| | | | | | and in fact now leads to incorrect permissions. Remove all instances of it from perl@ ports.
* - Update optionswen2015-06-281-7/+1
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* - Update to 3.6.11wen2015-06-282-15/+10
| | | | - Convert to optionsNG
* Use BROKEN helpersbapt2015-06-271-6/+2
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* Use BROKEN helpersbapt2015-06-271-5/+5
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* - Add LICENSEamdmi32015-06-251-1/+12
| | | | | | - Fix shebangs Approved by: porgmgr (bapt)
* Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. Theadamw2015-06-241-1/+0
| | | | | | downside to having this set is that portscout cannot find new releases when the username changes (which happens often in large projects with multiple maintainers).
* Convert to COPYTREE_SHAREbapt2015-06-231-9/+6
| | | | Use options helpers
* Convert to USES=jpegantoine2015-06-231-1/+1
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* - Fix shebangsamdmi32015-06-111-1/+3
| | | | MFH: 2015Q2
* New port: biology/bcftoolspi2015-06-0610-0/+178
| | | | | | | | | | | | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. WWW: http://www.htslib.org/ PR: 199747 Submitted by: cartwright@asu.edu
* - Strip binariesamdmi32015-06-041-1/+2
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* biology/mafft: update 7.149 -> 7.221robak2015-06-043-8/+7
| | | | | PR: 200603 Submitted by: Reed A. Cartwright <cartwright@asu.edu> (maintainer)
* - Add NO_ARCHamdmi32015-05-311-0/+1
| | | | Approved by: portmgr blanket
* - Fix shebangsamdmi32015-05-301-3/+9
| | | | | | | | - Add NO_ARCH - Add missing EXAMPLES option Approved by: portmgr blanket MFH: 2015Q2
* Update Unipro UGENE to version 1.16.2.danfe2015-05-283-3/+5
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* Remove $FreeBSD$ from patches files in categories a-j.mat2015-05-227-20/+0
| | | | | With hat: portmgr Sponsored by: Absolight
* biology/seaview: Update version 4.5.4=>4.5.4.4bofh2015-05-222-3/+4
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* - Update to 7.1.3wen2015-05-184-20/+22
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* - Update to 3.6.9 and unbreakwen2015-05-182-5/+3
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* MASTER_SITES cleanup.mat2015-05-143-7/+4
| | | | | | | | | | | | | | | | | | | - Replace ${MASTER_SITE_FOO} with FOO. - Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9% of the time.) - Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and no hint of what it should be was present. - Fix some logic. - And generally, make things more simple and easy to understand. While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and SAMBA macros. Also, replace some EXTRACT_SUFX occurences with USES=tar:*. Checked by: make fetch-urlall-list With hat: portmgr Sponsored by: Absolight
* - Update to 5.11.4wen2015-05-123-4/+10
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* Cleanup DIST* variables.mat2015-05-121-2/+1
| | | | | | | | | | | When appropriate: - Try to use DISTVERSION{SUF,PRE}FIX - Replace PORTNAME-PORTVERSION by DISTNAME - Convert MASTER_SITES to use macros - Other light cleanup With hat: portmgr Sponsored by: Absolight
* Reassign biology/ perl modules to perl@.adamw2015-05-098-21/+22
| | | | | | | | While here: Regenerate p5-AcePerl's patches using makepatch. Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the other way around. Bump PORTREVISION on those two ports.
* - Update to 36.3.7awen2015-05-073-6/+11
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* biology/seqtools: 4.33 -> 4.34.1pi2015-05-073-3/+7
| | | | | | | | | | | | | | Blixem - Added functionality to shift-select a range of coordinates, and copy the reference/match sequence for that range. - DNA search now highlights the resultant range of coordinates. - Added a splitter bar to allow the variations track to be resized. - Dotter Fix a crash pressing Esc on an undocked alignment or greyramp tool. - All Code reorganisation: the codebase is now in C++ rather than C, and a new module 'gbtools' has been created for generic utility functions.
* Update ports in the [bcd]* categories to not use GH_COMMIT.mat2015-05-064-7/+4
| | | | | | | With minor cleanups to make things simpler. With hat: portmgr Sponsored by: Absolight
* - Unbreakwen2015-05-042-2/+11
| | | | | PR: 199734 Submitted by: jwbacon@tds.net(maintainer)
* Mark BROKEN: fails to configureantoine2015-04-281-0/+2
| | | | | | | ===> Configuring for ncbi-blast+-2.2.30_2 configure: error: --localstatedir=/var: unknown option; use --help to show usage Reported by: pkg-fallout
* biology/ncbi-blast+: Add additionl MASTER_SITE to unbreak fetchmarino2015-04-251-3/+2
| | | | | | | | | The distfile was rerolled but nobody knows why (not a good sign). The maintainer has added a new MASTER_SITE with the original distfile in order to unbreak fetch. PR: 199474 Submitted by: maintainer (Jason Bacon)
* ${ENV} does not exist, it is called ${SETENV}.mat2015-04-131-1/+1
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* biology/seaview: Unbreak -- it fetches finemarino2015-04-111-4/+1
| | | | | | | | The second MASTER_SITES entry worked fine, so this must have been a transient fetch problem. I removed the first entry which is still failing though. Approved by: blanket
* biology/platon: Upgrade from 05 MAR 2015 => 30 MAR 2015 to unbreakmarino2015-04-112-6/+5
| | | | | | | | | As noted by previous commit, upstream rerolls the same distfile frequently. When FreeBSD cache was removed, the port broke. I'm fixing it again with a new digest, but I'm also defining DIST_SUBDIR, which is the correct thing to do with rerolls-by-policy. Also I removed the bad backup MASTER_SITES and tested in poudriere.
* biology/p5-Bio-ASN1-EntrezGene: bump PORTEPOCHmarino2015-04-111-0/+1
| | | | | | | Apparently in some world I don't live in 1.091 > 1.70 pkg needs this port's epoch to be bumped reported by: wen
* biology/p5-Bio-ASN1-EntrezGene: Upgrade 1.09 => 1.70 to unbreakmarino2015-04-113-15/+15
| | | | | | | While here, reset the port. The last time the maintainer was seen was in 2005, when the port was created. Also, rewrap the package description such that it keeps within 75 characters; also move the url so it won't wrap across lines.
* Update biology/paml to 4.8a and unbreak.brd2015-04-102-7/+5
| | | | | | PR: 199264 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: bdrewery (mentor)
* Convert bsd.gnustep.mk to USES=gnustepbapt2015-04-091-4/+2
| | | | | | | | | | | | | Simplify gnustep ports Hook into the regular ports framework: - LIB_DEPENDS for library dependencies - Use regular USE_LDCONFIG Reuse USES=objc (automatic) USE_GNUSTEP is now a macro to set the dependencies and build feature needed. Accepted arguments: back base build gui Merge deskutils/preferencepanes into deskutils/systempreferences
* Mark as broken unfetchable portsbapt2015-04-0610-0/+18
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* biology/ruby-bio: mark broken with ruby 2.2swills2015-04-031-1/+7
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* - Remove deprecated optionamdmi32015-04-021-9/+16
| | | | | | | | | - Tweak compiler flags - Add LICENSE - Pass maintainership to submitter PR: 199066 Submitted by: jwbacon@tds.net
* biology/seqtools: 4.32 -> 4.33pi2015-04-012-3/+3
| | | | | - Blixem/Dotter Multi-dotter support; may now start multiple dotters from blixem
* - Add LICENSEsunpoet2015-03-291-4/+6
| | | | - Space/Tab fix
* Upgrade from 3.6.6 to 3.6.7. Be sure to not extract the zlibmi2015-03-252-3/+4
| | | | subdirectory.
* 6 ports categories: Remove $PTHREAD_LIBSmarino2015-03-253-10/+8
| | | | | | Categories: cad, devel, java, x11-fm, biology, deskutils approved by: PTHREAD blanket
* biology/seaview: Update version 4.5.3.4=>4.5.4bofh2015-03-243-41/+5
| | | | - Remove dependency for libpdf as removed by upstream
* - Update to version 1.16.1danfe2015-03-233-8/+8
| | | | | | | - Explicitly list all required Qt components in USE_QT4 instead of relying on them being silently picked up through `www/webkit-qt4' dependency - Group *_build components together while here - Remove one REINPLACE_CMD call that is no longer needed
* biology/segan: Limit GCC to 4.8 while waiting for updatemarino2015-03-211-1/+1
| | | | | | | | | Due to questionable c++, GCC 4.9 and newer cannot build seqan. An update has been in the works that will enable clang compilers and all versions of GCC to build seqan, but it is not quite ready yet. While waiting for it, limit the version of GCC used to 4.8. PR: 196851
* For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME tobdrewery2015-03-211-2/+2
| | | | | | | | | | include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile having the same name despite changing one of these values and causing a bad checksum. Differential Revision: https://reviews.freebsd.org/D2103 Reviewed by: mat With hat: bdrewery
* Convert to new USE_GITHUB.mat2015-03-202-11/+4
| | | | | | While there, cleanup. Sponsored by: Absolight
* Fix packaging as a user (pkg already takes care of credentials)bapt2015-03-191-2/+2
| | | | Strip binaries
* - Simplify MASTER_SITESamdmi32015-03-171-3/+9
| | | | - Strip libraries
* biology/seaview: UNBREAKbofh2015-03-163-15/+38
| | | | | | | | | | - Update version 4.5.2=>4.5.3.4 - Add LICENSE (GPLv3) - Remove PDFLIBS as OPTIONS as it is no loner an optional requirement PR: 198602 Submitted by: pi Approved by: bapt marino (implicit)
* Some OCD cleanups on some of the perl@ ports.adamw2015-03-135-984/+976
| | | | | | | | | | | | | - Remove dependencies in core - Put testing depends in TEST_DEPENDS - Remove unnecessary bsd.port.options.mk inclusions - Remove checks for Perl versions that no longer exist in the ports tree - Sort plists, some of which were so jumbled that I have to assume the plist was randomized before committing A lot of the plist changes in this commit are moving PERL5_MAN3 after SITE_PERL. It's repo churn now, but it makes updating the ports later far easier.
* - Add empty directory to plistamdmi32015-03-111-0/+1
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* Update from 7.1.1 to 7.1.2.mi2015-03-112-3/+3
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* Unbreak by upgrading to March 5, 2015 "release" from upstream.mi2015-03-095-106/+103
| | | | | | | | | | | | Reduce restrictions from RESTRICTED to NO_CDROM -- the licensing allows use by academic community as long as it is not redistributed. Upstream still do not version their "releases", so next time they reroll the tarball, the download will start breaking again. But this time, it will be possible to fetch it from FreeBSD mirrors. Hide most of the optional data files under the DOCS-option and streamline various build-related scriptlets.
* Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors willmi2015-03-092-6/+4
| | | | | | | stop rerolling releases (and breaking downstream checksums) now. While here, allow parallel builds (seems to work again now) and stop extraction of unused subdirectories.
* biology/samtools: update 1.1 -> 1.2robak2015-03-062-4/+5
| | | | | PR: 198292 Submitted by: Reed Cartwright <cartwright@asu.edu>
* biology/htslib: update 1.1 -> 1.2.1robak2015-03-066-23/+45
| | | | | PR: 198291 Submitted by: Reed Cartwright <cartwright@asu.edu>
* Add a run dependency used by update_blastdb.plarved2015-03-061-1/+2
| | | | | PR: 198331 Submitted by: maintainer
* - Update to 1.13.10danilo2015-03-043-4/+4
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* Remove Authors from pkg-descrbapt2015-03-031-1/+0
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* Remove TEST dependency on p5-Test-Simple when the version in core isadamw2015-02-271-1/+0
| | | | | | sufficient. Thanks to az for showing me the light here.
* Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).danfe2015-02-243-9/+18
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* Mark BROKEN: Fails to link, tries to use internal fltk symbolsantoine2015-02-211-0/+2
| | | | | | | | | | | c++ -o seaview seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o \ -L/usr/local/lib -lfltk_images -lfltk \ -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama -L/usr/local/lib -lpdf \ -lX11 -lm -lz -pthread seaview.o: In function `clipboard_contains_alignment(char const*)': seaview.cxx:(.text+0x1c14): undefined reference to `fl_selection_buffer' Reported by: pkg-fallout
* biology/seqtools: 4.31 -> 4.32pi2015-02-122-3/+3
| | | | | | | | | | | | | | | - Blixem o Previously-unsupported GFF feature types can now be displayed as a new 'basic feature' type. o Styles are now applied to the detail view as well as the big picture, so feature display is more consistent across the two views. o Fix a bug where styles were not being applied to dynamically-loaded features. - Dotter o Added a 'maximise' button for the greyramp tool. o Small fixes to inconsistencies in context-sensitive menus and keyboard shortcuts.
* Mark BROKEN: Checksum and size mismatchantoine2015-01-311-0/+1
| | | | Reported by: pkg-fallout
* - Update to 3.6.6wen2015-01-313-5/+5
| | | | | PR: 197039 Submitted by: antont@inbox.lv
* - Update to 1.13.9danilo2015-01-313-4/+4
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* misc/otter & biology/ariadne: Not jobs safemarino2015-01-221-0/+2
| | | | | | The otter port tries to build libotter.a before an object is completely built (share.o in my case) and ariadne tries to start building in a directory before it is created (under multiple jobs).
* biology/py-biopython:makc2015-01-201-3/+5
| | | | | | - Convert to options framework Approved by: portmgr blanket
* Designatate 4 ports as unsafe for parallel buildingmarino2015-01-201-0/+1
| | | | | | All had similar errors that it couldn't find something during the build, yet built on a subsequent pass with no adjustments. Most I've seen before on previous bulk runs.
* - Pass maintainership to submitterwen2015-01-191-1/+1
| | | | | PR: 196859 Submitted by: Joseph Mingrone<jrm@ftfl.ca>
* - Simplify Makefilesunpoet2015-01-192-135/+130
| | | | | | - Use tab instead of space - Sort PLIST - Pass maintainership to perl@
* - Update to 1.13.8danilo2015-01-143-4/+4
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* Mark BROKEN: Unfetchableantoine2015-01-101-0/+1
| | | | Reported by: pkg-fallout
* Update to version 1.15.1.danfe2015-01-063-10/+10
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* biology/tinker: 6.2.6 -> 7.0.1pi2015-01-046-65/+94
| | | | | PR: 196376 Submitted by: Nikola Kolev <koue@chaosophia.net>
* - Convert USE_PYTHON -> USES leftovers missed in the previous commitsmva2015-01-041-1/+1
| | | | | Spotted by: antoine With hat: python
* Update to upstream version 36riggs2015-01-022-7/+6
| | | | | PR: 196339 Submitted by: koue@chaosophia.net
generated by cgit (git 2.34.1) at 2024-12-02 03:22:30 +0800