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* Fix the license text to make sense.Ettore Perazzoli2001-10-271-1/+0
* Update the licensing information to require version 2 of the GPLEttore Perazzoli2001-10-271-2/+2
* Update the copyrights, replacing Helix Code with Ximian andEttore Perazzoli2001-06-231-2/+2
* Ask for a folder to import into.Iain Holmes2001-05-121-0/+33
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path: root/biology
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* biology/diamond: Update to version 0.9.17jrm2018-02-042-4/+4
* - Update to 3.3.20180129wen2018-02-042-5/+4
* Multiple ports:jwb2018-02-0416-29/+16
* devel/boost-*: update to 1.66.0jbeich2018-02-042-1/+2
* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSdanfe2018-02-041-2/+4
* Update Qt5 ports to 5.9.3.rakuco2018-02-041-0/+10
* biology/seaview: Update version 4.6.2=>4.6.3bofh2018-02-043-7/+8
* New USES=eigentcberner2018-02-041-5/+2
* - Update to 3.697wen2018-02-042-3/+4
* - Update to 5.16.0wen2018-02-043-4/+9
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1jrm2018-02-042-3/+4
* biology/iqtree: Update to version 1.6.1jrm2018-02-042-9/+8
* Disable the extra flag "-march=native" on arm to fix builds.linimon2018-02-041-3/+6
* Update to 2.0.1sunpoet2018-02-043-5/+31
* biology/canu: Replace += with = for dependsjwb2018-02-041-2/+2
* - Fix build on 11+amdmi32018-02-042-4/+11
* [new port] biology/canu: Single molecule sequence assemblerjwb2018-02-046-0/+167
* Try to bring some consistency to ports that have x86-specific pieces.linimon2018-02-042-12/+12
* Switch from swig 2.0 to swig 3.0bapt2018-02-041-2/+4
* Mark more recently failing ports broken on aarch64.linimon2018-02-041-2/+3
* Back out previous commits by jbeich demand.linimon2018-02-042-10/+2
* Bah. Remove spare line from cut-and-paste.linimon2018-02-041-1/+0
* Attempt to fix build on non-x86 archs. Untested, but does no harmlinimon2018-02-042-2/+11
* biology/diamond: Update to version 0.9.14jrm2018-02-042-4/+4
* biology/seqtools: re-try on powerpc* after r449590jbeich2018-02-041-2/+0
* - Those ports fail to build with python3antoine2018-02-041-1/+1
* Mark several ports newly broken on arm.linimon2018-02-042-3/+9
* biology/py-biom-format: Add required dependency on math/py-pandas and dojrm2018-02-041-3/+7
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adap...jwb2018-02-045-0/+47
* These are also broken on aarch64 in the same way as armv6/7.linimon2018-02-041-0/+1
* Mark more ports broken that fail on both armv6 and armv7.linimon2018-02-041-0/+3
* Revert previous fat-fingered commit. These are the error messages fromlinimon2018-02-041-2/+2
* Update errror message on armvX.linimon2018-02-041-2/+2
* biology/fasttree: update to version 2.1.10jwb2018-02-044-19/+45
* biology/py-macs2: Restrict to python 2.7.jwb2018-02-041-2/+2
* Add a USES=python:env, that will not add a dependency on Python.mat2018-02-042-4/+2
* Fix configure options for gnustep-maketheraven2018-02-041-1/+1
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)...jwb2018-02-044-0/+41
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ...jwb2018-02-045-0/+91
* Fix packaging with python3antoine2018-02-042-14/+14
* [unbreak] biology/bwa: Remove old patch filesjwb2018-02-043-37/+0
* [new port] biology/fastqc: Quality control tool for high throughput sequence ...jwb2018-02-045-0/+260
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentjwb2018-02-041-1/+0
* Convert Python ports to FLAVORS.mat2018-02-049-17/+15
* For ports that are marked BROKEN on armv6, and also fail to build onlinimon2018-02-045-0/+5
* biology/bowtie2: Upgrade to 2.3.3.1jwb2018-02-045-50/+19
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, pojwb2018-02-045-0/+74
* biology/bwa: Upgrade to 0.7.17jwb2018-02-042-5/+10
* biology/vcftools: Upgrade to latest release 0.1.15jwb2018-02-042-4/+4
* - Switch to options helpersamdmi32018-02-041-1/+5
* biology/diamond: Update to version 0.9.13jrm2018-02-042-4/+4
* - Update to 3.1b2wen2018-02-045-39/+69
* Fix the context of some patches so that they apply with stricter patch(1)antoine2018-02-042-6/+6
* biology/diamond: Update to version 0.9.12jrm2018-02-042-7/+5
* Fix USE_GITHUB usage.mat2018-02-042-5/+4
* biology/py-pysam: Update to 0.13yuri2018-02-042-6/+8
* biology/diamond: Update to 0.9.11jrm2018-02-043-10/+14
* biology/molden: chase another intransparent upstream distfile upgrade.jmd2018-02-042-4/+4
* - Fix installing scripts and support binarieswen2018-02-044-8/+39
* Update biology/py-pysam to 0.12.0.1tcberner2018-02-042-4/+4
* biology/htslib biology/bcftools biology/samtools: Update to 1.6pizzamig2018-02-0425-897/+171
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofjrm2018-02-041-1/+13
* New port, biology/iqtree: Efficient phylogenomic softwarejrm2018-02-044-0/+43
* Mark as broken ports with no public distfilesbapt2018-02-046-1/+10
* Remove dead master sitesbapt2018-02-042-2/+3
* biology/molden: unbreak by chasing latest intransparent distfile update.jmd2018-02-042-4/+4
* devel/boost-*: update to 1.65.1jbeich2018-02-041-1/+1
* devel/boost-*: enable C++11 featuresjbeich2018-02-041-1/+1
* biology/ssaha: unbreak with gcc7jbeich2018-02-041-0/+9
* Remove USES=execinfo.mat2018-02-042-2/+2
* Update tbb to 2018 and bump dependent ports' revisionsmartymac2018-02-041-1/+1
* Update to 1.007002sunpoet2018-02-043-23/+5
* Add p5-Bio-FeatureIO 1.6.905sunpoet2018-02-045-0/+67
* Fix license information for portgs that use "the same license as Perl".mat2018-02-0410-10/+10
* - Update to 1.007002wen2018-02-043-15/+4
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-02-0415-15/+15
* Update to 3.3.20170530sunpoet2018-02-042-3/+5
* Remove expired ports:rene2018-02-045-87/+0
* Update GNUstep core libraries.theraven2018-02-041-1/+1
* - update to 1.70wen2018-02-042-4/+4
* biology/diamond: Update to version 0.9.10jrm2018-02-042-4/+4
* - Update to 1.53wen2018-02-042-4/+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 rapidmiwi2017-05-06