diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/HTSeq/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/HTSeq/metadata.xml | 8 | ||||
| -rw-r--r-- | sci-biology/Manifest.gz | bin | 23653 -> 23647 bytes | |||
| -rw-r--r-- | sci-biology/STAR/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/STAR/metadata.xml | 8 | ||||
| -rw-r--r-- | sci-biology/bamtools/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/bamtools/metadata.xml | 8 | ||||
| -rw-r--r-- | sci-biology/bcftools/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/bcftools/metadata.xml | 4 | ||||
| -rw-r--r-- | sci-biology/bedtools/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/bedtools/metadata.xml | 11 | ||||
| -rw-r--r-- | sci-biology/foldingathome/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/foldingathome/foldingathome-7.6.9.ebuild | 140 | ||||
| -rw-r--r-- | sci-biology/kallisto/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/kallisto/metadata.xml | 8 | ||||
| -rw-r--r-- | sci-biology/mafft/Manifest | 8 | ||||
| -rw-r--r-- | sci-biology/mafft/files/mafft-7.037-respect.patch | 217 | ||||
| -rw-r--r-- | sci-biology/mafft/files/mafft-7.305-fno-common.patch | 8 | ||||
| -rw-r--r-- | sci-biology/mafft/mafft-7.050.ebuild | 60 | ||||
| -rw-r--r-- | sci-biology/mafft/mafft-7.215.ebuild | 64 | ||||
| -rw-r--r-- | sci-biology/mafft/mafft-7.305.ebuild | 3 |
21 files changed, 160 insertions, 401 deletions
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest index aea46b37a979..7112b7eebe07 100644 --- a/sci-biology/HTSeq/Manifest +++ b/sci-biology/HTSeq/Manifest @@ -1,4 +1,4 @@ DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 EBUILD HTSeq-0.9.1.ebuild 696 BLAKE2B b24c94dec95e472577986eddaadf778b72e2b4fc1155198bedac99ba4c2bb444220c2f872ea6c48a20afe6b0f5230c63f0265c5b9bff5fd588e6c57ff65a6c07 SHA512 7eca88cfd432bc799ad91fedb0f0b998a948a3e8c3bdfff33c7b3fee3a19276eb5cfe99a09609a179e415833798abb28d27e716f04dd1513b24406b79b9a8be9 EBUILD HTSeq-9999.ebuild 696 BLAKE2B b24c94dec95e472577986eddaadf778b72e2b4fc1155198bedac99ba4c2bb444220c2f872ea6c48a20afe6b0f5230c63f0265c5b9bff5fd588e6c57ff65a6c07 SHA512 7eca88cfd432bc799ad91fedb0f0b998a948a3e8c3bdfff33c7b3fee3a19276eb5cfe99a09609a179e415833798abb28d27e716f04dd1513b24406b79b9a8be9 -MISC metadata.xml 555 BLAKE2B 9cb1b8a7b9beeeb137209a73b0f4687f3134f08ac17119daddcdff8f12c74b5724ea45e1de7a5259b1ffa39c06f103e1280065a72b26d73576bad377ed5c86b9 SHA512 a9402ce0e04f242a4509d6f8e3bfc998b32703a9e1ac619d618d761f03e76a92eb5ab625bba7b72dabf23d36d587d48815652764e9f62b317482495ecf59a97e +MISC metadata.xml 329 BLAKE2B f06dd42c6a1d3bca399cbe48d519346519b9acb0e4176ee79657e058ad1724b542242704e5cc3237873f338b1b23887715f95673957e533c057464ef07e8634f SHA512 04b82836732bf1415d6ce9d3b4c75139aa7d96382da2fd3343a54053172cffcac9ce96dab49b91852dea1a2a38b73cd90279c2c86496577bd6a79040a1fb6026 diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml index 8d3c9ccebe2a..1b5a1245ecb9 100644 --- a/sci-biology/HTSeq/metadata.xml +++ b/sci-biology/HTSeq/metadata.xml @@ -1,14 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 279c5e1ae791..c80adb185621 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest index 0a455535a7d7..d95ade6caf13 100644 --- a/sci-biology/STAR/Manifest +++ b/sci-biology/STAR/Manifest @@ -1,4 +1,4 @@ AUX STAR-2.5.3a-fix-build-system.patch 5318 BLAKE2B 28a839eb61a5b1adef804249328c7917dca2ec765f00a48b90aa42d7da3ca393f7726b7aafdb6d0429a55fe696bd51b0e06d85ef6e50a3a4f5874c731b194f1e SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441 DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf EBUILD STAR-2.5.3a.ebuild 881 BLAKE2B 692466b512aaa3da2e2323f90576d47c2f5e694a4ac8ee8ce2d887435a1ef964dcab9adbdb3c3f88b43cc5463b258635be0f2b542485ee16bc9ec32b655fcf65 SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663 -MISC metadata.xml 566 BLAKE2B 615699c5b86e5cd75ec3de91e19d9e6d479198bbbe43045f017cc8ed52576931b159870c35bcdc4fd02a0de1e3ab2aa3eb9f17984b783865fb2f9e3a31f11858 SHA512 15055f76fab8b0d47fc79c85706bc0e58d577ac0572696628139facb672d3384d2ee9629b69f07a009c3dedb83e94ae35ee9749fc841369cd1ad3cac2d6e6920 +MISC metadata.xml 340 BLAKE2B af4a68a2c7b9b584b5ce2ec685a88fa9cd42fa0088d3fcb12d4030b03ac59b375da75c04c59f0969f6c3d922085786e990fa574fd54cba30a7fc7fa2d89f4861 SHA512 83e9732928a44ad6bc92168b8a9319be9b5211489cbbe6e78ab92bfc33817c73a2c16f1336737da38a136ea81e6ed2cccd9a007a5ae13752b2bb8765ef6f891a diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml index 10ecc35730e0..def338693901 100644 --- a/sci-biology/STAR/metadata.xml +++ b/sci-biology/STAR/metadata.xml @@ -1,14 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest index eaed3ef7be55..edf34d69a5ba 100644 --- a/sci-biology/bamtools/Manifest +++ b/sci-biology/bamtools/Manifest @@ -1,4 +1,4 @@ DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb EBUILD bamtools-2.5.1.ebuild 773 BLAKE2B 58b5af7760648a6919a875736cc52e851e9ff30cb5b308bdfd69a014e67e74a857f8f5a46c5f9d8e398b25383b3b316bfddf3b0fa3b09ca845ef31d87aab3e76 SHA512 7be431719d95ee3e44e79e752d201a940974cc343d20cba8e743a9e6566d6958abefa93f72fafab020d354fc84a42ab68ff131253375c442b91949e175860ff6 EBUILD bamtools-9999.ebuild 773 BLAKE2B 58b5af7760648a6919a875736cc52e851e9ff30cb5b308bdfd69a014e67e74a857f8f5a46c5f9d8e398b25383b3b316bfddf3b0fa3b09ca845ef31d87aab3e76 SHA512 7be431719d95ee3e44e79e752d201a940974cc343d20cba8e743a9e6566d6958abefa93f72fafab020d354fc84a42ab68ff131253375c442b91949e175860ff6 -MISC metadata.xml 881 BLAKE2B e7feabf909d8dbccc784cd2e94d07882d700433e773ac51928b796f4bfd22a7e8de7a4d99268dd8ea0f8d36683f5bbe9f3c4fcba37fc85c284f49b9ad7d413e0 SHA512 4922e3edaa65c7981b8656245287e4c4d613f8ba6d6b63131fe9e5183f8119eab5501e354ad80d37d8f61f56d86513af2aedd2b086e5da3d1ab48b3aef57a18c +MISC metadata.xml 643 BLAKE2B 80a4127e1186ff37b02f8baa15eb45584da61eef96e83bfa59c39035c868baee4b39e0157f4ccd797de2f09a0ab85f217631065b82efe53a9919db1dc06d1058 SHA512 dee93787f3016396b3883d9c2c4c5e8ad6f1043e94cdecb7b0210b2cc5883ceace4f4eaf41d80fd1f917af543399de058988d349885402d4847c6505da62837e diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index f703e6a82899..9aa0cee0cf72 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -1,18 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> <upstream> <remote-id type="github">pezmaster31/bamtools</remote-id> diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 7c2dc6eb8a68..c247c7af050a 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -6,4 +6,4 @@ DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a31905 DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c EBUILD bcftools-1.5.ebuild 868 BLAKE2B acfd6758e27cb9ade023d91074724affd0fa3016af565c809819fae615be61ca8af90edf6b38eaf0a4ed5f3e9eaaa19451096b8d7c27a58c6ed0540bf7260784 SHA512 e0aacba5fc54cbf7a8d64db84e52f28baf8df36fa01c63fc167998c6ec5ef65a040c0725f445970f32888ae947b89d50d92dc2fc704fdf63a8a900762ec367e6 EBUILD bcftools-1.9-r2.ebuild 1000 BLAKE2B eb5e7bb5f33f5ef22594eb241f3900ee6a6c125cb83b0e425732fbd6d781dac382b1664281e3256587ea8f344db578c1ec778ac2d5ae4794fa67931468cb580c SHA512 90d56585baae31be060fc8a54de5d86c1bd015da187d86a37ceee1176a685a864214e124770dfb895d568bb57e143f9a35b7f627f36598dbf4cb544119f2185d -MISC metadata.xml 452 BLAKE2B 53a356b0569d9db1377bc1881d58b4b354d4861eb21b2c602df59b7923b175a20623cf3369695416eb08d44fabe32036f5a5ec3119c765c8f85347d3b094918a SHA512 eb656430c9ee5ffee5ec5f9f8f3c69e8b0d1ae124cd720ae4af6c3c160da5dc261838744f75e838a85935bbc9bd5201b038ee11cb41a0e1209c9df58aa85fc1a +MISC metadata.xml 343 BLAKE2B e1664c6d67ebde81b9f99b69d442e0b16891ecd392fddd55ed2aaa885dcb2f4ca39cd627cd3f6367f39b13e35eb1141119e53756d6efc4ac62c819ab1d611633 SHA512 cfa167a5733f40d7e36e9e229229acd883ba7bfd812afb9060c742c505354b1c754070e2e897a48d7611a123b9606b6f43a0816c089e71bf64f3d0dbd8b7184d diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index a1fb64db6fe9..0421097960c1 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -5,10 +5,6 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> <upstream> <remote-id type="github">samtools/bcftools</remote-id> </upstream> diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 9c73c14bcb7b..8d91db427f4f 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,4 +1,4 @@ DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def EBUILD bedtools-2.26.0.ebuild 959 BLAKE2B c3d42f033913e18a9bd1f0b6f669a4000bc6b6892bbd5986a33a99ed496ae4af11b690f1c7c350644b62e77baef80a9eb52f15e87818a74b684d4fac816a2512 SHA512 a3914d04806fa4b3f14f83d91717d00fd183e1f6d4a39690ae04e7767791605a8e90d86cefc4deaa50327651c64125808658de4471f05df936c19e46768bf988 -MISC metadata.xml 761 BLAKE2B 35d57919e32a4b8bd6070ab5a513f62578394d43098d9e7b9b0765fd57d684c049dad9ec1b315044518bf01535d505e9d9d3fee540308df40c0b70886db8e49f SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770 +MISC metadata.xml 406 BLAKE2B 5a16830031644c5087241b9e20afcb6315095c877e2b019eace76ee0602929c168c2273e27e99f03ca3c1a57db0bf728c2d8ccc39b7f80588bb215d1fd6a3ea6 SHA512 35a9b50a772503e6691faf1e2f1093bd6ffd5f6f5be08b1ad8581948f4f3e8fb7e54faa101cff757fc561ed71696253114c32fb6293df59cda3e8fd7c24d2bb0 diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index 39869a9f2790..ec82800df5dd 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -1,21 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> - <longdescription> - BEDTools: a flexible suite of utilities for comparing genomic features. - </longdescription> <upstream> <remote-id type="google-code">bedtools</remote-id> <remote-id type="github">arq5x/bedtools2</remote-id> diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest index 71fe4a3400d5..a3762634a224 100644 --- a/sci-biology/foldingathome/Manifest +++ b/sci-biology/foldingathome/Manifest @@ -1,4 +1,6 @@ AUX 7.3/folding-conf.d 339 BLAKE2B 93a0b3672777ad737ce27694aaca547634c375e180ad3c28c3adb9cae2cb1c054ff9458ee1fe04b70fe9841ae67d41198bcecfc4826d05d5de8df2759bd80910 SHA512 6fd10dc938262c05831e68176e93a24869bb6991508bcc48ece487b701788026561d073025bd347cd77ede13ca26f6b284861f30b07becf72ea77e4db22867b3 DIST fahclient_7.5.1-64bit-release.tar.bz2 3438239 BLAKE2B 69fb60cdd5356fe4f5ad1f106b67d078baf0394c5d3c474dff2f1ac840bcb31bfd9ca9a9c6112b9ee9497dcdc223732627a21c50b455e46c096a52587d5d229b SHA512 5f6f2f882d57fe53ad0a55b48f09fc3803af6aebbbf0e92be39477d4c4da92237d6edabec61dd8183678bdcfe3923ff9b0938647a77edc2c69ce8958defcfdf1 +DIST fahclient_7.6.9-64bit-release.tar.bz2 3962851 BLAKE2B 896ca7cdd1357bb37cd8a5c438223c398c5f8c6bde7f7302d0e62ccff603b9a3dd3fb348bd021b9654867eb8f2579c91cfe87e3229b365620b383a4f261ae5f4 SHA512 0a360d8a985d3d538922a2d9519b70845a568f7d052c3047e7f847865165e9cd6e741016ee00496161ca3c2115beef34e95ab594d0f864bccc0fe12de6886f19 EBUILD foldingathome-7.5.1-r3.ebuild 4454 BLAKE2B 9103461fe2614c5494648827b461cc488e7345f3ad12d45ccda6c44c81de7f700120d582b3ab4371974a5a25a62626b535849e8bafa13ac577c59364102cb7a3 SHA512 4c1a451a5df2e2015594f266761d51b9ac0978711ce93f4bc922937a0fa474bdead787926541ad42d554130cf6168e367f8c090648d52951ca6b7f1533c042f2 +EBUILD foldingathome-7.6.9.ebuild 4422 BLAKE2B 50f39d12b3c1bf23e94119a7d3a1434f7f44e1765ab77550e4561875be2e1b5b8ca1e00393ba1b218ebb12f54b4cc27721ee46586986b8771b8216ab6fe20e33 SHA512 1be3543d064a478e22abf386bdc634f5e63710aaada32fd035b4f5c1ef02bc01521a084430e9cc4fed17a677b51a62d811f5c74b1dca1b581b489f585d5d58ee MISC metadata.xml 360 BLAKE2B c0ef2b11cc9e6498a420dcd2e6c83ee71f7e286c3e78218257c56350bd2c0921732d48cc4207a31bcfd965a4a9dca65e9bdc4d62831dc430e86541d36fc691f8 SHA512 687f1516a8ec80270fa173b0a7d7c259f3f02ffefa69d3175b72e170bd11aeb786563edb43214390a83b6b61b1231e2734124e50bb2a523d1a564bc3b143f00b diff --git a/sci-biology/foldingathome/foldingathome-7.6.9.ebuild b/sci-biology/foldingathome/foldingathome-7.6.9.ebuild new file mode 100644 index 000000000000..ca477a6d6b77 --- /dev/null +++ b/sci-biology/foldingathome/foldingathome-7.6.9.ebuild @@ -0,0 +1,140 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit user systemd + +DESCRIPTION="Folding@Home is a distributed computing project for protein folding" +HOMEPAGE="https://foldingathome.org/" +SRC_URI="https://download.foldingathome.org/releases/public/release/fahclient/centos-6.7-64bit/v$(ver_cut 1-2)/fahclient_${PV}-64bit-release.tar.bz2" + +RESTRICT="mirror bindist strip" + +LICENSE="FAH-EULA-2014 FAH-special-permission" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" +# Expressly listing all deps, as this is a binpkg and it is doubtful whether +# i.e. uclibc or clang can provide what is necessary at runtime +DEPEND="dev-util/patchelf" +RDEPEND="app-arch/bzip2 + || ( + dev-libs/openssl-compat:1.0.0 + =dev-libs/openssl-1.0*:* + ) + sys-devel/gcc + sys-libs/glibc + sys-libs/zlib + acct-group/video +" + +S="${WORKDIR}/fahclient_${PV}-64bit-release" + +QA_PREBUILT="opt/foldingathome/*" + +pkg_setup() { + elog "" + elog "Special permission is hereby granted to the Gentoo project to provide an" + elog "automated installer package which downloads and installs the Folding@home client" + elog "software. Permission is also granted for future Gentoo installer packages on the" + elog "condition that they continue to adhere to all of the terms of the accompanying" + elog "Folding@home license agreements and display this notice." + elog "-- Vijay S. Pande, Stanford University, 07 May 2013" + elog "" + elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )" + elog "" + + enewgroup foldingathome + enewuser foldingathome -1 -1 "${EPREFIX}"/opt/foldingathome video +} + +src_install() { + patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHClient || die + patchelf --set-rpath "${EPREFIX}/opt/foldingathome" FAHCoreWrapper || die + + dosym "../../usr/$(get_libdir)/libssl.so.1.0.0" /opt/foldingathome/libssl.so.10 + dosym "../../usr/$(get_libdir)/libcrypto.so.1.0.0" /opt/foldingathome/libcrypto.so.10 + + exeinto /opt/foldingathome + doexe {FAHClient,FAHCoreWrapper} + + insinto /opt/foldingathome + doins sample-config.xml + + newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome + cat <<EOF >"${T}"/fah-init +#!/sbin/openrc-run +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\"" +command="${EPREFIX}/opt/foldingathome/FAHClient" +command_args="\${FOLD_OPTS}" +command_user=foldingathome +command_background=1 +pidfile="\${PIDFILE}" +EOF + newinitd "${T}"/fah-init foldingathome + + cat <<EOF >"${T}"/fah-init.service +[Unit] +Description=Folding@Home V7 Client +Documentation=https://foldingathome.org + +[Service] +Type=simple +User=foldingathome +Group=foldingathome +Nice=19 +WorkingDirectory=${EPREFIX}/opt/foldingathome +ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false +NoNewPrivileges=yes +PrivateTmp=yes +ProtectControlGroups=yes +ProtectSystem=full +RestrictRealtime=true +ProtectControlGroups=yes + +[Install] +WantedBy=multi-user.target +EOF + systemd_newunit "${T}"/fah-init.service foldingathome.service + + fowners -R foldingathome:foldingathome /opt/foldingathome +} + +pkg_postinst() { + elog "To run Folding@home in the background at boot:" + elog "(openrc)\trc-update add foldingathome default" + elog "(systemd)\tsystemctl enable foldingathome" + elog "" + if [ ! -e "${EPREFIX}"/opt/foldingathome/config.xml ]; then + elog "No config.xml file found -- please run" + elog "emerge --config ${P} to configure your client, or specify" + elog "all necessary runtime options in FOLD_OPTS within" + elog "${EPREFIX}/etc/conf.d/foldingathome" + elog "" + fi + if [[ -n ${REPLACING_VERSIONS} ]]; then + elog "NOTE, the 'initfolding' helper script has been dropped, please" + elog "use emerge --config ${P} or run FAHClient --configure directly" + elog "and adjust file permissions and ownership yourself" + elog "" + fi + elog "Please see ${EPREFIX}/opt/foldingathome/FAHClient --help for more details." + einfo "" + einfo "The original package maintainer encourages you to acquire a username and join team 36480." + einfo "http://folding.stanford.edu/English/Download#ntoc2" + einfo "" +} + +pkg_postrm() { + elog "Folding@home data files were not removed." + elog "Remove them manually from ${EPREFIX}/opt/foldingathome" +} + +pkg_config() { + cd "${EPREFIX}"/opt/foldingathome || die + su foldingathome -s /bin/sh -c "./FAHClient --configure" +} diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest index 761cca70e40a..b7356e9ae1b6 100644 --- a/sci-biology/kallisto/Manifest +++ b/sci-biology/kallisto/Manifest @@ -1,4 +1,4 @@ DIST kallisto-0.43.1.tar.gz 1067076 BLAKE2B 15a2fc65f0c9db431d9be6b2c8434b582ff7bf95fb659a9838d287feb3486744bca6201563d0f318be47c0f8532b805148a2eabfda633075d6b55bad1c3a406a SHA512 c7725a2d649cf96fcd24a20d542b409777cfd9fe97c09f0f459a5ec2981e0a4f5f0ea03d76d3ec3edf0e498c799fc7d074d442d5e35ddb4043d1f7634619dda8 EBUILD kallisto-0.43.1.ebuild 573 BLAKE2B 895c8ccecb6b882cde7672208bf070f1b0de70ad15fadce89e0296f87a93d011a3de096d548bdb3e788e215767a7f6e0673c160fe82fb50fb4256653f9901a39 SHA512 bb8667422d4015ca7a3aad912385b5322b83c1122a99f79893f527c886cbc05049f2e37f7cc85d2c789994ebd477b9ff60019e4c91b7b95f65a51dd7343c4aff EBUILD kallisto-9999.ebuild 573 BLAKE2B 895c8ccecb6b882cde7672208bf070f1b0de70ad15fadce89e0296f87a93d011a3de096d548bdb3e788e215767a7f6e0673c160fe82fb50fb4256653f9901a39 SHA512 bb8667422d4015ca7a3aad912385b5322b83c1122a99f79893f527c886cbc05049f2e37f7cc85d2c789994ebd477b9ff60019e4c91b7b95f65a51dd7343c4aff -MISC metadata.xml 574 BLAKE2B 6f48c88742a02cd19d181593a85b6c17e03d85cf47f8db9dc8696edc0d1cb8f47afda663a88e0b2f213dcc5ae59a9ec157d55dd68547b9c7ebad2cc1a5612d67 SHA512 322d73b8e377ce74593d5c79a4e2f2041ab9313d8d5f59866e148ccda89892fd4fe56a7f0c8d12458f97de52efc4e933044788ad24fd99ffd4fb81dbbc2b2bcc +MISC metadata.xml 345 BLAKE2B de5a80ed6236a16fe08fb6a7eb815379edfa12af65db8c96a92b7494e8633661167152e1579fa886a13cc8060f0a68ac2646bc0a2321ce1fb39f9585bdc95511 SHA512 162700e5baed9b4696b90ecd014af596dca15a21bb27ffac4bc945c51701ec18e5cae963341670eb679873dfb54e22bfb9cb39299a5a00639e6afc6fd9f80412 diff --git a/sci-biology/kallisto/metadata.xml b/sci-biology/kallisto/metadata.xml index aba0d0ebf330..03ad8ef865a9 100644 --- a/sci-biology/kallisto/metadata.xml +++ b/sci-biology/kallisto/metadata.xml @@ -1,14 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <maintainer type="project"> - <email>proxy-maint@gentoo.org</email> - <name>Proxy Maintainers</name> - </maintainer> <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest index b5bb9dcd4893..974e08b0ca57 100644 --- a/sci-biology/mafft/Manifest +++ b/sci-biology/mafft/Manifest @@ -1,8 +1,4 @@ -AUX mafft-7.037-respect.patch 7463 BLAKE2B a7218e21a08452aab65ea544cfff91a0a88f3400e667cbe945848cba7507b678e9c1d1f03bdb4b4b3b1d7b43df2a3f2097090f588274c04f6ecfe53436149245 SHA512 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fe9de41eaea3bf799065fac88b336ec45af3c5b4d7d5272a477d99165b88c27f7e7765908e7955eaa0a74bb59df10a0ab77b822fd29bebca601d124938f3489d DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9 -EBUILD mafft-7.050.ebuild 1796 BLAKE2B 7377a5d75e2c0d61e9502e16c8a61d5031f12adcbfb53ba58e1ec0ef7a7eab730aa0bbfbc1c7f6da77b185e5eb429300bd8c997e31dea9927738fc2b31c764cd SHA512 2c5e8078a76c44ccc8151b6493f74038ed2e7bdff336fdebe4171d87c34a3664d2b794030198f798606231c13d3b4b0dabc101c429b438c3675f3909d93a1c1e -EBUILD mafft-7.215.ebuild 1976 BLAKE2B e490252063bc448db647d0de765c49c468bc2b395b06c2fa26b6368d8d5e26eceb99204f879f0d3104930881393e3f99ecfc9a915b936f299863750cfceb656d SHA512 f297da061416bdbbb3d7ebcaa4efe62b88cb7ca8eedcf0eeaf61fcfb8af42f7dd8b1cbec270ae247efd7a4c7c95ee04a44903d26116e4b73e87ea9fe349d38fa -EBUILD mafft-7.305.ebuild 2015 BLAKE2B baae93bd674fc22dcbdc14c728c1bd30216f6d94aaceef3b0889ced8fb5b9f55114d03f9a84679f8dfcb54db630a4ff70df538af46b33da2251345b657bdab89 SHA512 c5102f225b1bbe7b89d497e14a78c742f05e873c73a9947669c125bda951d59806da697a29134b639043fef49375a1bb73aeb935445a1e698124fdb78ddb6004 +EBUILD mafft-7.305.ebuild 2067 BLAKE2B 679f6b2270aa60b51416b4f1cf3322a217db912d98a84397134064035b21151b9a20c5ab387f0d671365f8c8abecee924cade70ade9a5174c1e24f8e3d08a7c1 SHA512 d3781c854315146303f8702b4f80ce0ce1de9e543a8e85fb267be27b422a8eeba716f21353853d4e618ae89635bb993f12f446c625a7e6b5e79807b967202b01 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch deleted file mode 100644 index 6fba7153622d..000000000000 --- a/sci-biology/mafft/files/mafft-7.037-respect.patch +++ /dev/null @@ -1,217 +0,0 @@ - core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- - 1 file changed, 50 insertions(+), 50 deletions(-) - -diff --git a/core/Makefile b/core/Makefile -index 9acebb3..3838a45 100644 ---- a/core/Makefile -+++ b/core/Makefile -@@ -145,151 +145,151 @@ mltaln.h : functions.h - touch mltaln.h - - version : version.c mltaln.h -- $(CC) -o $@ version.c $(MYCFLAGS) -+ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) - - tbfast : $(OBJTBFAST) -- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) - - addsingle : $(OBJADDSINGLE) -- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) - - tbfast2 : $(OBJTBFAST2) -- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) - - disttbfast : $(OBJDISTTBFAST) -- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) - - makedirectionlist : $(OBJMAKEDIRECTIONLIST) -- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) - - splittbfast : $(OBJSPLITTBFAST) -- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) - - splitfromaln : $(OBJSPLITFROMALN) -- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) - - splittbfast2 : $(OBJSPLITTBFAST2) -- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) - - dummy : $(OBJDUMMY) -- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) - - setcore : $(OBJSETCORE) -- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) - - countlen : $(OBJCOUNTLEN) -- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) - - seq2regtable : $(OBJSEQ2REGTABLE) -- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) - - regtable2seq : $(OBJREGTABLE2SEQ) -- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) - - setdirection : $(OBJSETDIRECTION) -- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) - - replaceu : $(OBJREPLACEU) -- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) - - restoreu : $(OBJRESTOREU) -- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) - - f2cl : $(OBJF2CL) -- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) - - mccaskillwrap : $(OBJMCCASKILLWRAP) -- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) - - contrafoldwrap : $(OBJCONTRAFOLDWRAP) -- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) - - pairlocalalign : $(OBJPAIRLOCALALIGN) -- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) - - pairash : $(OBJPAIRASH) -- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) - - rnatest : $(OBJRNATEST) -- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) - - pair2hat3s : $(OBJPAIR2HAT3S) -- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) - - multi2hat3s : $(OBJMULTI2HAT3S) -- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) - - getlag : $(OBJGETLAG) -- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) - - tditr : $(OBJTDITR) -- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) - - dvtditr : $(OBJDVTDITR) -- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) - - mafft-profile : $(OBJGALN) -- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) - - gapfill : $(OBJGAPFILL) -- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) - - dndfast4 : $(OBJDNDFAST4) -- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) - - dndfast5 : $(OBJDNDFAST5) -- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) - - dndfast6 : $(OBJDNDFAST6) -- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) - - dndfast7 : $(OBJDNDFAST7) -- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) - - dndblast : $(OBJDNDBLAST) -- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) - - dndfast3 : $(OBJDNDFAST3) -- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) - - triplet : $(OBJTRIPLET) -- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) - - triplet3 : $(OBJTRIPLET3) -- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) - - sextet3 : $(OBJSEXTET3) -- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) - - sextet4 : $(OBJSEXTET4) -- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) - - sextet5 : $(OBJSEXTET5) -- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) - - mafft-distance : $(OBJDISTANCE) -- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) - - triplet5 : $(OBJTRIPLET5) -- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) - - triplet6 : $(OBJTRIPLET6) -- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) - - octet4 : $(OBJOCTET4) -- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) - - dndpre : $(OBJDNDPRE) -- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) - - dndpre2 : $(OBJDNDPRESCORE) -- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) - - score : $(OBJSCORE) -- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) - - genMtx : $(OBJGENMTX) -- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) - - gapfill.o : gapfill.c $(HEADER) - $(CC) $(MYCFLAGS) -c gapfill.c -@@ -525,7 +525,7 @@ install : all - chmod 755 $(SCRIPTS) - $(INSTALL) $(SCRIPTS) $(BINDIR) - chmod 755 $(PROGS) -- $(INSTALL) -s $(PROGS) $(LIBDIR) -+ $(INSTALL) $(PROGS) $(LIBDIR) - $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) - - ( cd $(BINDIR); \ diff --git a/sci-biology/mafft/files/mafft-7.305-fno-common.patch b/sci-biology/mafft/files/mafft-7.305-fno-common.patch new file mode 100644 index 000000000000..0287b6367f8b --- /dev/null +++ b/sci-biology/mafft/files/mafft-7.305-fno-common.patch @@ -0,0 +1,8 @@ +--- a/core/mltaln.h ++++ b/core/mltaln.h +@@ -336,4 +336,4 @@ + + extern double sueff_global; + extern double lenfaca, lenfacb, lenfacc, lenfacd; +-int maxl, tsize; ++extern int maxl, tsize; diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild deleted file mode 100644 index 5da5d12d1b31..000000000000 --- a/sci-biology/mafft/mafft-7.050.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib toolchain-funcs - -EXTENSIONS="-without-extensions" - -DESCRIPTION="Multiple sequence alignments using a variety of algorithms" -HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" -SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}"/${P}${EXTENSIONS} - -src_prepare() { - epatch "${FILESDIR}"/${PN}-7.037-respect.patch - use threads && append-cppflags -Denablemultithread - sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die - sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" -} - -src_compile() { - pushd core > /dev/null || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ - PREFIX="${EPREFIX}"/usr \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" - popd > /dev/null || die -} - -src_test() { - export MAFFT_BINARIES="${S}"/core - cd test || die - bash ../core/mafft sample > test.fftns2 || die - bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die - bash ../core/mafft --globalpair sample > test.gins1 || die - bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die - bash ../core/mafft --localpair sample > test.lins1 || die - bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die - - diff test.fftns2 sample.fftns2 || die - diff test.fftnsi sample.fftnsi || die - diff test.gins1 sample.gins1 || die - diff test.ginsi sample.ginsi || die - diff test.lins1 sample.lins1 || die -} - -src_install() { - pushd core - emake PREFIX="${ED}usr" install - popd - dodoc readme -} diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild deleted file mode 100644 index 05c3d8d52399..000000000000 --- a/sci-biology/mafft/mafft-7.215.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib toolchain-funcs - -EXTENSIONS="-without-extensions" - -DESCRIPTION="Multiple sequence alignments using a variety of algorithms" -HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" -SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}"/${P}${EXTENSIONS} - -src_prepare() { -# epatch "${FILESDIR}"/${PN}-7.037-respect.patch - use threads && append-cppflags -Denablemultithread -# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die - sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" - sed \ - -e 's:$(LDFLAGS)::g' \ - -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ - -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ - -e '/INSTALL/s: -s : :g' \ - -i core/Makefile || die -} - -src_compile() { - cd core || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ - PREFIX="${EPREFIX}"/usr \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" -} - -src_test() { - export MAFFT_BINARIES="${S}"/core - cd test || die - bash ../core/mafft sample > test.fftns2 || die - bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die - bash ../core/mafft --globalpair sample > test.gins1 || die - bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die - bash ../core/mafft --localpair sample > test.lins1 || die - bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die - - diff test.fftns2 sample.fftns2 || die - diff test.fftnsi sample.fftnsi || die - diff test.gins1 sample.gins1 || die - diff test.ginsi sample.ginsi || die - diff test.lins1 sample.lins1 || die -} - -src_install() { - dodoc readme - cd core || die - emake PREFIX="${ED}usr" install -} diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild index 9f9f631416b2..f4863892571a 100644 --- a/sci-biology/mafft/mafft-7.305.ebuild +++ b/sci-biology/mafft/mafft-7.305.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -17,6 +17,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" IUSE="threads" S="${WORKDIR}/${P}${EXTENSIONS}" +PATCHES=( "${FILESDIR}"/${PN}-7.305-fno-common.patch ) src_prepare() { default |