aboutsummaryrefslogtreecommitdiffstats
path: root/biology
Commit message (Expand)AuthorAgeFilesLines
* Mark several ports newly broken on arm.linimon2017-12-112-3/+9
* biology/py-biom-format: Add required dependency on math/py-pandas and dojrm2017-12-101-3/+7
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adap...jwb2017-12-095-0/+47
* These are also broken on aarch64 in the same way as armv6/7.linimon2017-12-091-0/+1
* Mark more ports broken that fail on both armv6 and armv7.linimon2017-12-091-0/+3
* Revert previous fat-fingered commit. These are the error messages fromlinimon2017-12-081-2/+2
* Update errror message on armvX.linimon2017-12-081-2/+2
* biology/fasttree: update to version 2.1.10jwb2017-12-054-19/+45
* biology/py-macs2: Restrict to python 2.7.jwb2017-12-051-2/+2
* Add a USES=python:env, that will not add a dependency on Python.mat2017-12-042-4/+2
* Fix configure options for gnustep-maketheraven2017-12-031-1/+1
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)...jwb2017-12-034-0/+41
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ...jwb2017-12-035-0/+91
* Fix packaging with python3antoine2017-12-012-14/+14
* [unbreak] biology/bwa: Remove old patch filesjwb2017-12-013-37/+0
* [new port] biology/fastqc: Quality control tool for high throughput sequence ...jwb2017-12-015-0/+260
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentjwb2017-12-011-1/+0
* Convert Python ports to FLAVORS.mat2017-11-309-17/+15
* For ports that are marked BROKEN on armv6, and also fail to build onlinimon2017-11-305-0/+5
* biology/bowtie2: Upgrade to 2.3.3.1jwb2017-11-305-50/+19
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, pojwb2017-11-305-0/+74
* biology/bwa: Upgrade to 0.7.17jwb2017-11-282-5/+10
* biology/vcftools: Upgrade to latest release 0.1.15jwb2017-11-282-4/+4
* - Switch to options helpersamdmi32017-11-261-1/+5
* biology/diamond: Update to version 0.9.13jrm2017-11-182-4/+4
* - Update to 3.1b2wen2017-11-115-39/+69
* Fix the context of some patches so that they apply with stricter patch(1)antoine2017-11-102-6/+6
* biology/diamond: Update to version 0.9.12jrm2017-11-092-7/+5
* Fix USE_GITHUB usage.mat2017-11-062-5/+4
* biology/py-pysam: Update to 0.13yuri2017-11-062-6/+8
* biology/diamond: Update to 0.9.11jrm2017-11-033-10/+14
* biology/molden: chase another intransparent upstream distfile upgrade.jmd2017-11-012-4/+4
* - Fix installing scripts and support binarieswen2017-10-304-8/+39
* Update biology/py-pysam to 0.12.0.1tcberner2017-10-262-4/+4
* biology/htslib biology/bcftools biology/samtools: Update to 1.6pizzamig2017-10-2525-897/+171
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofjrm2017-10-221-1/+13
* New port, biology/iqtree: Efficient phylogenomic softwarejrm2017-10-224-0/+43
* Mark as broken ports with no public distfilesbapt2017-10-136-1/+10
* Remove dead master sitesbapt2017-10-132-2/+3
* biology/molden: unbreak by chasing latest intransparent distfile update.jmd2017-09-282-4/+4
* devel/boost-*: update to 1.65.1jbeich2017-09-251-1/+1
* devel/boost-*: enable C++11 featuresjbeich2017-09-251-1/+1
* biology/ssaha: unbreak with gcc7jbeich2017-09-251-0/+9
* Remove USES=execinfo.mat2017-09-222-2/+2
* Update tbb to 2018 and bump dependent ports' revisionsmartymac2017-09-171-1/+1
* Update to 1.007002sunpoet2017-09-163-23/+5
* Add p5-Bio-FeatureIO 1.6.905sunpoet2017-09-165-0/+67
* Fix license information for portgs that use "the same license as Perl".mat2017-09-1510-10/+10
* - Update to 1.007002wen2017-09-133-15/+4
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2017-09-1115-15/+15
* Update to 3.3.20170530sunpoet2017-09-042-3/+5
* Remove expired ports:rene2017-08-235-87/+0
* Update GNUstep core libraries.theraven2017-08-211-1/+1
* - update to 1.70wen2017-08-182-4/+4
* biology/diamond: Update to version 0.9.10jrm2017-08-162-4/+4
* - Update to 1.53wen2017-07-232-4/+4
* Deprecate ports BROKEN for more than 6 monthsantoine2017-07-221-0/+2
* biology/seaview: Update version 4.6.1=>4.6.2bofh2017-07-222-4/+4
* Chase next distfile update. Upstream contacted whether we would be allowed to...jmd2017-07-142-4/+4
* biology/molden: Unbreak by chasing their latest opaque update to the distribu...jmd2017-07-122-7/+5
* Update math/gsl to 2.4tcberner2017-07-041-1/+1
* biology/diamond: Update to version 0.9.9jrm2017-07-042-4/+4
* Update devel/readline to 7.0 patch 3sunpoet2017-06-271-1/+1
* Begin deorbit burn of ia64. We have not attempted to build packages forlinimon2017-06-251-1/+1
* Mark BROKEN.mat2017-06-221-0/+2
* biology/diamond: Update to version 0.9.8jrm2017-06-162-4/+4
* - Update WWWamdmi32017-06-102-8/+7
* - Update to 0.11.2.2wen2017-06-102-4/+4
* Previous commit unbroke the port.linimon2017-06-031-2/+0
* biology/diamond: Update to version 0.9.4jrm2017-06-032-4/+4
* Remove outdated PERL_LEVEL checksunpoet2017-06-021-8/+2
* Remove outdated PERL_LEVEL checksunpoet2017-06-021-8/+2
* Update WWWsunpoet2017-05-301-1/+1
* biology/diamond: Update to version 0.9.3jrm2017-05-292-4/+4
* Mark some ports failing on armv6, for errors classified as "clang".linimon2017-05-271-0/+2
* Mark some ports failing on armv6, for errors classified as "???".linimon2017-05-272-3/+6
* biology/molden: Chase recent upstream change of molden distfile.jmd2017-05-242-4/+4
* - Update to 0.11.2.1joneum2017-05-242-5/+5
* biology/diamond: Update to version 0.9.1jrm2017-05-232-6/+6
* Revision bump of all ports with USE_GL after consolidation of mesa-libsrezny2017-05-233-3/+3
* It is possible that r441426 will fix the build problem on armv6. Givelinimon2017-05-221-1/+0
* Mark some ports failing on power64. In cases where the error messagelinimon2017-05-221-0/+2
* Mark BROKEN: checksum and size mismatchantoine2017-05-201-0/+2
* - Update to 5.15.0wen2017-05-183-3/+14
* Mark some ports failing on power64. In cases where the error messagelinimon2017-05-135-3/+6
* - Update to 0.11.1miwi2017-05-082-4/+4
* - Update to 1.5.1miwi2017-05-072-6/+4
* bx-python is a python library and associated set of scripts to allow for rapidmiwi2017-05-064-0/+47
* pysam is a lightweight wrapper of the htslib C-API and provides facilities tomiwi2017-05-065-0/+47
* - Update to 1.69wen2017-05-032-4/+4
* devel/boost-*: update to 1.64.0jbeich2017-05-021-1/+1
* Update math/gsl to 2.3tcberner2017-05-021-0/+1
* Provide error messages for some ports failing on aarch64, and, in alinimon2017-05-022-0/+5
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (goog...ler2017-04-305-79/+0
* biology/py-biom-format: Update to version 2.1.6jrm2017-04-292-4/+5
* - Fix shebangsmiwi2017-04-221-2/+3
* - Fix shebangsmiwi2017-04-221-3/+4
* - Fix shebangsamdmi32017-04-221-3/+7
* biology/diamond: Update to version 0.8.38jrm2017-04-212-6/+5
* biology/seaview: Update version 4.6=>4.6.1bofh2017-04-122-4/+5
* biology/diamond: Update to version 0.8.37jrm2017-04-022-5/+5
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andgerald2017-04-0116-11/+16
* Update devel/tbb to 2017.5martymac2017-03-071-0/+1
* Mark the remaining ports depending on Google Code as DEPRECATED, with anmat2017-03-041-0/+2
* - Update to 1.42wen2017-03-012-4/+4
* Fix USE_GITHUB's GH_TAGNAME usage.mat2017-02-282-5/+5
* biology/plinkseq: unbreak with clang 4.0jbeich2017-02-272-0/+12
* biology/bowtie2: update to 2.3.0jbeich2017-02-274-6/+48
* Mark a few more ports that create large logfiles broken on armv6.linimon2017-02-261-0/+2
* Mark various ports as broken on armv6: invokes x86 asm.linimon2017-02-262-0/+2
* - Update to 1.14.9danilo2017-02-253-6/+12
* Move -fPIC to where Linux puts it so it is limited to a single library.tijl2017-02-142-4/+2
* biology/diamond: Update to version 0.8.36.jrm2017-02-122-4/+4
* biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.jmd2017-02-112-7/+5
* Add -fPIC to various ports to enable them to build on armv6.linimon2017-02-101-8/+3
* - Mark BROKEN: does not fetch, size/checksum mismatchamdmi32017-02-071-0/+2
* Update to 1.5.1sunpoet2017-02-072-9/+8
* biology/diamond: Update to version 0.8.35.jrm2017-02-062-5/+5
* Move devel/rubygem-bio to biology/rubygem-biosunpoet2017-02-054-0/+36
* Bump PORTREVISION for ports affected by the fix the last commit.mat2017-02-013-1/+3
* Mark various ports broken on aarch64 and armv6.linimon2017-01-311-0/+2
* biology/diamond: Update to version 0.8.34.jrm2017-01-232-4/+4
* Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/sunpoet2017-01-213-3/+3
* biology/diamond: Update to version 0.8.32.jrm2017-01-162-4/+4
* biology/diamond: Update to version 0.8.31.jrm2017-01-132-4/+4
* - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOLamdmi32017-01-092-15/+3
* devel/boost-*: update to 1.63.0jbeich2017-01-061-1/+1
* Never set WRKSRC when using USE_GITHUB.mat2017-01-042-4/+0
* Assume "pkg-config zlib" works after 9.x reached EOLjbeich2017-01-041-3/+0
* Remove BROKEN_FreeBSD_9sunpoet2017-01-012-3/+0
* biology/diamond: Update to version 0.8.30jrm2016-12-312-4/+4
* biology/ncbi-blast+: Add MAKE_JOBS_UNSAFEjrm2016-12-231-0/+2
* - Update to 1.007001sunpoet2016-12-212-4/+4
* biology/bowtie2: Update to version 2.2.9jrm2016-12-212-14/+18
* biology/cd-hit: Update to bug-fix release 4.6.6jrm2016-12-212-5/+4
* biology/jellyfish: Update to version 2.2.6jrm2016-12-203-54/+56
* - Update *_DEPENDS: Bio::Coordinate family has been moved from biology/p5-Bio...sunpoet2016-12-191-2/+4
* - Add p5-Bio-Coordinate 1.007001sunpoet2016-12-195-0/+58
* - Update to 1.007000sunpoet2016-12-194-20/+29
* - Update to 1.007001sunpoet2016-12-196-383/+180
* - Update to 2.5.0wen2016-12-195-68/+190
* - Update to 2.40sunpoet2016-12-183-10/+22
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-Runsunpoet2016-12-186-8/+10
* - Add LICENSE_FILEsunpoet2016-12-181-2/+5
* - Add LICENSEsunpoet2016-12-181-4/+8
* - Add LICENSEsunpoet2016-12-181-1/+7
* - Move biology/p5-bioperl to biology/p5-BioPerlsunpoet2016-12-187-9/+7
* biology/diamond: Update to version 0.8.29jrm2016-12-182-4/+4
* biology/protomol: Support build with C++11 (taken from dports)marino2016-12-185-0/+48
* biology/blat: Fix build on DF (taken from dports)marino2016-12-181-0/+14
* biology/lamarc: Fix build on DF (taken from dports)marino2016-12-181-0/+11
* biology/chemeq: fix build on GCC (taken from dports)marino2016-12-181-0/+11
* Remove libintl.so.9 compatibility link that was added in r374303 totijl2016-12-093-2/+3
* Remove libjpeg.so.11 compatibility link that was added in r374303 totijl2016-12-091-0/+1
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andgerald2016-12-077-5/+7
* biology/molden: distfile was updated in xwin.cpi2016-12-042-4/+4
* Do not use post-stage. Use post-install instead.mat2016-12-021-1/+1
* biology/njplot: Add site in MASTER_SITES because package builders arejrm2016-11-281-2/+4
* biology/diamond: Update to version 0.8.28jrm2016-11-282-5/+6
* Fixup USE_GITHUB usage.mat2016-11-262-3/+3
* Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the defaultgerald2016-11-261-1/+1
* devel/boost-*: update to 1.62.0jbeich2016-11-231-0/+1
* - Remove unnecessary USES=shebangfixsunpoet2016-11-211-4/+8
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andgerald2016-11-205-2/+5
* biology/avida: Fix ncurses from ports supportmarino2016-11-191-1/+3
* biology/njplot: Revive and update to version 2.4jrm2016-11-165-0/+109
* Mark various leaf ports broken on aarch64, and, where appropriate, otherlinimon2016-11-114-2/+8
* Attempt to fix build on non-x86 archs.linimon2016-11-111-3/+5
* biology/seqtools: update 4.43.0 -> 4.44.1pi2016-11-113-4/+14
* biology/molden: add missing LICENSE_NAMEpi2016-11-101-1/+2
* biology/molden: fix distinfo, set LICENSEpi2016-11-102-7/+11
* The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.linimon2016-11-093-3/+3
* Mark as broken on arm64.linimon2016-11-081-0/+2
* Mark broken on all tier-2 archs.linimon2016-11-081-0/+3
* Mark broken on the rest of the tier-2 archs: invokes x86 asm.linimon2016-11-081-1/+4
* biology/diamond: Update to version 0.8.26jrm2016-11-062-4/+4
* Cleanup no longer needed CHMOD usage after r424898.mat2016-11-034-12/+5
* - Mark it BROKENwen2016-10-281-1/+3
* Use USES=pathfix where applicable.mat2016-10-214-21/+11
* ${RM} already has -f.mat2016-10-213-3/+3
* biology/diamond: update to version 0.8.24jrm2016-10-172-4/+4
* biology/diamond: update to version 0.8.23jrm2016-10-102-4/+4
* Mark BROKEN: unfetchable, size mismatchantoine2016-10-011-0/+1
* biology/blat: Fix build with non-base SSLmarino2016-10-011-4/+4
* Update PORTREVISION and dinstinfo due to upstream tarball changejrm2016-09-302-3/+4
* biology/paml: update to version 4.9c and various improvementsjrm2016-09-284-33/+48
* Update email address to jrm@FreeBSD.org for ports that I maintainjrm2016-09-243-5/+3
* - Update to 1.68wen2016-09-232-3/+4
* - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]pawel2016-09-156-28/+39
* GOOGLE_CODE has gone away.mat2016-09-141-0/+2
* - Update to 0.8.22amdmi32016-09-142-4/+4
* biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)marino2016-09-111-3/+2
* - Update to 1.72wen2016-09-112-4/+4
* Most commonly used build systems support silent builds, when theyamdmi32016-09-101-1/+1
* - Make configure script handle --disable-silent-rules gracefullyamdmi32016-09-061-1/+1
* - Update to 0.8.20wen2016-09-062-4/+4
* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withtijl2016-09-062-4/+3
* biology/molden: 5.4 -> 5.7pi2016-08-262-6/+4
* Update to version 0.8.19pawel2016-08-262-4/+4
* - Mark BROKEN: does not fetch (distfile was removed from ftp)amdmi32016-08-221-0/+2
* biology/bedtools is not jobs safemarino2016-08-221-0/+2
* - Switch to options helpersamdmi32016-08-183-16/+11
* Update biology/diamond to 0.8.18.brd2016-08-152-4/+4
* - Update to 1.9 [1]wen2016-08-082-10/+8
* Update to version 0.8.17pawel2016-08-062-5/+5
* biology/seqtools: 4.42.1 -> 4.43.0pi2016-07-313-17/+227
* Update to upstream release 0.8.16riggs2016-07-252-4/+4
* Cleanup $() variables in ports Makefiles.mat2016-07-201-1/+1
* - update libgd to 2.2.2dinoex2016-07-201-1/+1
* When there is a do-install target, do not use a post-install target, domat2016-07-193-4/+5
* Trim excess tabs, no-op changepawel2016-07-151-13/+13
* Update to version 0.8.14pawel2016-07-152-4/+4
* - Update to 0.8.11amdmi32016-07-072-5/+5
* Remove expired ports without open PRs:rene2016-07-057-161/+0
* - LICENSEamdmi32016-07-022-10/+22
* biology/diamond: update 0.8.6 -> 0.8.9junovitch2016-06-302-4/+4
* - Add missing dependency, fixing buildamdmi32016-06-241-1/+5
* - Switch to options helpersamdmi32016-06-212-7/+11
* biology/diamond: update to 0.8.6rm2016-06-182-4/+4
* - Fix run-time dependency issuesolivierd2016-06-111-2/+13
* biology/seaview: Update version 4.5.4.8=>4.6bofh2016-06-102-7/+4
* Update to 0.8.5matthew2016-06-093-34/+18
* - Update to 1.35wen2016-06-082-3/+4
* Remove unneeded usage of:mat2016-06-061-2/+1
* Deprecate ports broken for more than 6 monthsantoine2016-06-042-0/+4
* - Do install cmake and pkgconfig modulesamdmi32016-05-282-3/+8
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1pi2016-05-278-20/+23
* Remove useless WRKSRC definitions.mat2016-05-251-2/+0
* - Fix trailing whitespace in pkg-messagesamdmi32016-05-196-12/+12
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*amdmi32016-05-1921-36/+36
* Fix DEPENDSantoine2016-05-191-2/+2
* - Convert to USES=mysqlamdmi32016-05-171-8/+4
* - Update to 4.9aamdmi32016-05-172-4/+7
* biology/bowtie2: 2.2.7 -> 2.2.8pi2016-05-142-3/+3
* Prevent collision with getline(3)bapt2016-05-141-0/+300
* Prevent collision with getline(3)bapt2016-05-141-0/+291
* Prevent collision with getline(3)bapt2016-05-124-6/+27
* biology/seqan: update 1.3.1 -> 2.1.1junovitch2016-05-1012-1915/+3706
* New port: biology/seqan-appsjunovitch2016-05-105-0/+220
* Add final slash in WWW entryolivierd2016-05-101-1/+1
* The BIOM file format (canonically pronounced biome) is designed to be aolivierd2016-05-104-0/+48
* During the exp-run in bug 208158, it was found that biology/ugene givesdim2016-05-084-0/+36
* DNA query sequences against a protein reference database (BLASTP and BLASTXwen2016-05-065-0/+71
* - Update to 1.14.8danilo2016-05-013-4/+4
* biology/seqtools: 4.41.1 -> 4.42.1pi2016-04-232-5/+5
* many ports: mark broken on powerpc64swills2016-04-221-0/+2
* - Switch to options helpersamdmi32016-04-173-16/+17
* - Update to 1.66wen2016-04-172-4/+3
* - Switch to options helpersamdmi32016-04-161-3/+8
* Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:mi2016-04-163-4/+5
generated by cgit (git 2.34.1) at 2024-11-16 02:29:56 +0800