From 9ee6d97c2883d42f204a533a8bc1f4562df778fb Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 16 Sep 2020 09:32:48 +0100 Subject: gentoo resync : 16.09.2020 --- sci-biology/Manifest.gz | Bin 23341 -> 23330 bytes sci-biology/biopython/Manifest | 2 +- sci-biology/biopython/biopython-1.77.ebuild | 2 +- sci-biology/bowtie/Manifest | 10 - sci-biology/bowtie/bowtie-1.1.2-r1.ebuild | 74 ---- .../files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch | 17 - .../files/bowtie-1.1.2-fix-setBegin-call.patch | 42 --- .../bowtie/files/bowtie-1.1.2-seqan-popcount.patch | 24 -- .../bowtie-1.1.2-seqan-rename-ChunkPool.patch | 382 --------------------- .../bowtie-1.1.2-seqan-rename-fill-to-resize.patch | 85 ----- .../bowtie/files/bowtie-1.1.2-spelling.patch | 48 --- .../bowtie-1.1.2-tbb-tinythread-missing.patch | 18 - .../bowtie/files/bowtie-1.1.2-unbundle-seqan.patch | 27 -- sci-biology/embassy/Manifest | 2 +- sci-biology/embassy/embassy-6.6.0-r1.ebuild | 30 -- sci-biology/embassy/embassy-6.6.0-r2.ebuild | 29 ++ sci-biology/exonerate/Manifest | 2 +- sci-biology/exonerate/metadata.xml | 3 - sci-biology/finchtv/Manifest | 2 +- sci-biology/finchtv/metadata.xml | 3 - sci-biology/libgtextutils/Manifest | 2 +- sci-biology/libgtextutils/metadata.xml | 2 +- sci-biology/seqan/Manifest | 11 +- .../seqan/files/seqan-1.4.2-buildsystem.patch | 30 -- sci-biology/seqan/files/seqan-1.4.2-include.patch | 16 - sci-biology/seqan/files/seqan-1.4.2-shared.patch | 22 -- sci-biology/seqan/seqan-1.4.2-r1.ebuild | 79 ----- sci-biology/seqan/seqan-2.2.0-r1.ebuild | 94 ----- sci-biology/seqan/seqan-2.4.0.ebuild | 25 +- sci-biology/seqan/seqan-9999.ebuild | 25 +- 30 files changed, 54 insertions(+), 1054 deletions(-) delete mode 100644 sci-biology/bowtie/bowtie-1.1.2-r1.ebuild delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch delete mode 100644 sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch delete mode 100644 sci-biology/embassy/embassy-6.6.0-r1.ebuild create mode 100644 sci-biology/embassy/embassy-6.6.0-r2.ebuild delete mode 100644 sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch delete mode 100644 sci-biology/seqan/files/seqan-1.4.2-include.patch delete mode 100644 sci-biology/seqan/files/seqan-1.4.2-shared.patch delete mode 100644 sci-biology/seqan/seqan-1.4.2-r1.ebuild delete mode 100644 sci-biology/seqan/seqan-2.2.0-r1.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index fb1ebe38a141..cf12f63f683b 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 0141c7450dbb..963e867595db 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,3 +1,3 @@ DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5 -EBUILD biopython-1.77.ebuild 1855 BLAKE2B 739e5cc4a954ac9cc5fe0640ac5f418ad1ee1aadb66570a41996e8e260dc75c8c4373c94b53b0d147d1b661169c1aa3352b9367ab0e37cfd8bd05c220186ac92 SHA512 e2dd1ef79804c779645162410e6890d0618d080ac20195cae0097fe3a42c204d270321949e8d5056b85f9e9a5ed598e05c20f2869178dd16ea86ea105167271a +EBUILD biopython-1.77.ebuild 1859 BLAKE2B 84f27ea48f70afb396f0670f41606e646872e0b4ed1596141bdc51c5432f048b75300e9ec74b430255eacea118cf717287294cb67e34faa82757d00793ceeb5f SHA512 0de36036de4e246f7c9dbde30c14c7a29016cc6ae28e8809ee1c95a150add413a19ab84c6ba1fc7b9344f900db4e93c040a90989ccce9c5f10ea9f426bffd189 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/biopython/biopython-1.77.ebuild b/sci-biology/biopython/biopython-1.77.ebuild index 486e9fe694d1..a25abc9312c6 100644 --- a/sci-biology/biopython/biopython-1.77.ebuild +++ b/sci-biology/biopython/biopython-1.77.ebuild @@ -5,7 +5,7 @@ EAPI=7 PYTHON_COMPAT=( python3_{6..9} ) -inherit distutils-r1 eutils +inherit distutils-r1 optfeature DESCRIPTION="Python modules for computational molecular biology" HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index bbf916477036..f9a42acddbb3 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,14 +1,4 @@ -AUX bowtie-1.1.2-_ContextLss-1.1-1.4.patch 601 BLAKE2B 36de166ef2f22d6a6cf9a5773d62f74bd69241b2a788f376108f847f09be0811b4c0156e8a5ded0e0f724cdffa77ed0b79ade064c0268b91ff966319ac2c0d0d SHA512 e39ec6323cc6fee49a6ecf3565066d9cb8f8001af2701de292025f268d57dcfa3d4c35f3e2aed56b7e3835a955e5bfb595214ac232309fcc46c6d51f83cd9f2e -AUX bowtie-1.1.2-fix-setBegin-call.patch 1269 BLAKE2B 3bfa4fca8a94c600f6d405c4824cc83ac5838c0353f3e36417bdb1e88222902f786fe6f8e3e5099f577ca5044b2caf5d9eaf64876311ea9df4a5d4314bd22f03 SHA512 8838a0d8b35c9ceb4be1ef3439eab5e3478dcfe11c5e59e327717676eceab413b07ec97dbda9fb3527ab61653a8a6e2d651b5bb4c24114288d3b07922348c5d3 -AUX bowtie-1.1.2-seqan-popcount.patch 566 BLAKE2B 6d9d109fbbba2b85d22c923959ca0726cb9bb2da950b0b0b9aa84106c9b74c24d5bf997d1339273f92cffc5bf42c9852bf376dce260c1374c3374f8f230e395d SHA512 07b70a1941b98033967b8a7303fab94aa3a047bd5da9355f58f03af04f4515903cbf2698700fb3e987546998ebb28225672aa8fbfc65dd8bc202be8a26290838 -AUX bowtie-1.1.2-seqan-rename-ChunkPool.patch 11618 BLAKE2B bc4e9610bdde7dba741c7963c59f0361cca43e6224d1c4f2448d53111cbb0ac2d0cbd45a8d90948689bf0af1c511f180839a0b981c1588dda2f52f3a2e06a0d6 SHA512 3d05ea37c753c780163123ab8fdf8d149f0daddf4c52fcf81b1380951f132edf312b13505ea9afc2ff34ee4f3188b5251beb9e71e3c78f2eeabfadd4ab1ae5a1 -AUX bowtie-1.1.2-seqan-rename-fill-to-resize.patch 3280 BLAKE2B 00815454c116bc8b64a96668508fdddbf9909aefea84353031524eef479e60a540ed74512ca7c4e62d41e6bea4bed60cf102621390070b4f45bc63abcb2b20dd SHA512 e0a96c870670c6c38b48da0c0e0f3dc4f5e9b0654ecb1d55c22484472192cc926168a333625a582c470e2781f6e062d6704723feb29d7f32f2a19eb229622aa0 -AUX bowtie-1.1.2-spelling.patch 4157 BLAKE2B 2a48f2da1e68df166230fe35f9858b34b86962d97ec7d36a9bc0b19615961623ff2403dc630dae4cb2d4ade439b4b487762ac7be32efb7947dee3b2bb919d7a1 SHA512 1679ecdaffa55adb2c1e206a77eba6052e4d9e65e476f73df795bf1fc9e323d34c20f4673a285701b067c65477b3804cd44a4c30b36ae5502f534a4cf191af18 -AUX bowtie-1.1.2-tbb-tinythread-missing.patch 554 BLAKE2B 745629aa93f2e74191b944345b95b4d2e4e399a9e5c5a0f48690d3abe411076e4f71603333ff70050af8c63c2a9dcb753d1e9ceb1fa2ec066b9002a7f71ea96f SHA512 04cc9dad3a6c2598bde41975604a75ca5f0b1490144d2a9f91c049b04b8af80d95e8842aaf1b551ec3d9ca842981e72aa692f00b80971c067d7464776c1e78c9 -AUX bowtie-1.1.2-unbundle-seqan.patch 751 BLAKE2B d9689b298f21f4619dbbed96b58d8ae7fc5f646539ae33291222d282153b545ad6fb3e30fe1ba5f0f452e2f3e7e9706b6761f5d4184dcd5ad96a55ccc7b246be SHA512 9a68ccc98774a2c9ddb8f45b5ed009230d14d3e29837c6dd8aac34e298f57208361ef45d0e7d9d074495f3465b58f08606cced9e4fccb549785591ff954cb2b8 AUX bowtie-2.2.9-fix-c++14.patch 687 BLAKE2B a75f473f429379789a97142d7820fb19fc1a64b764236c6fa1c068cefb03e37a58b41b0a515a62d42e85b3131f0dfe8f2bb856126528099277394674a0e53248 SHA512 3aa6e7a30fdf93ae564091ce9b87338ab9feccbd0c873f4130af71dc94fd3b27527b42a93f13471a2613bad44dbacd639d17515000f03856695a0021ce14dfc5 -DIST bowtie-1.1.2-src.zip 7713258 BLAKE2B ac10aca905099b5a70d3fab6f90e2dc4713bf7b460d027abf89a6ef6103979724e70b2915a86ffa571b59dcd9df768c80be1846cccd08f7f85dd402ce64c0cb0 SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205 -EBUILD bowtie-1.1.2-r1.ebuild 1643 BLAKE2B 81f79b8b8d9b9a56061bf92df193a21e2db03bdacb6290020e8fb2426e3e1cf9e5a6a802cb6fa5f5f68be8d7f92f749e14c0c3528ebad5825d3927bcf33ca483 SHA512 8b5c22f29aafb5977313ea002fcd654ac991015f7808f02f8e02c2105dd9a6fa77b5f5342e82d38b07674c93dbe397333be78f6d1ca9a24a60531d6a40efe382 EBUILD bowtie-2.2.9.ebuild 1277 BLAKE2B b9cf9edc34af3f01eb1cde1510637bbcbaf7206d9a24135d859d14dcefe793abd0b78dd19dbcd1835840514e754061aee86a79d5992ca68d316c64c98bb4891c SHA512 40e22698d5df241b8b98c601f8ed22276d39f4c9818bb23afec0a39b625fd38a0fdb3f4b4d6f8c01b458e2b6b3464a7ee8a135bd446f3488354eeca9934daa85 MISC metadata.xml 528 BLAKE2B 310fb406a0dbe56b194ae13cf521264e105f9d849b09e10d5d7e556c7d00a9cc7a0f9546a91e43f30344c9ec14a76e0d8a3f037fb4cb91bba68999d9f45b69e0 SHA512 1eb83cbd7d7e747bc94021051ba6ae0bf22411091287b754851a9f6824b263b6ca83c9a0d055c0b6ab24963ceea9b32d76bf1b343f48a3ee4bd322fec539b301 diff --git a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild b/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild deleted file mode 100644 index d8b607f870fc..000000000000 --- a/sci-biology/bowtie/bowtie-1.1.2-r1.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - sci-biology/seqan:1.4 - app-arch/unzip" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( - "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" - "${FILESDIR}/${P}-fix-setBegin-call.patch" - "${FILESDIR}/${P}-seqan-popcount.patch" - "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" - "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" - "${FILESDIR}/${P}-spelling.patch" - "${FILESDIR}/${P}-tbb-tinythread-missing.patch" - "${FILESDIR}/${P}-unbundle-seqan.patch" -) - -src_prepare() { - default - - # remove bundled libraries, use system seqan 1.4 - rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -} diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch b/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch deleted file mode 100644 index 78b9c01a0462..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Change class name of _Context_LSS - New version 1.4 of SeQan uses a different name of the class. -Forwarded: no -Author: Gert Wollny -Last-Update: 2014-100-06 - ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -856,7 +856,7 @@ void DifferenceCoverSample::build( - { - Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); - VMSG_NL(" Invoking Larsson-Sadakane on ranks"); -- _Context_LSS c; -+ ContextLss_ c; - c.suffixsort( - (TIndexOff*)begin(_isaPrime, Standard()), - (TIndexOff*)begin(sPrime, Standard()), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch b/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch deleted file mode 100644 index af7f7f61cd5e..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-fix-setBegin-call.patch +++ /dev/null @@ -1,42 +0,0 @@ -Description: Proper type-casting in using seqan::_setBegin(). - Required by newer versions of GCC. -Forwarded: no -Author: Ognyan Kulev -Last-Update: 2013-04-18 - ---- a/pat.h -+++ b/pat.h -@@ -82,20 +82,20 @@ struct ReadBuf { - ~ReadBuf() { - clearAll(); reset(); - // Prevent seqan from trying to free buffers -- _setBegin(patFw, NULL); -- _setBegin(patRc, NULL); -- _setBegin(qual, NULL); -- _setBegin(patFwRev, NULL); -- _setBegin(patRcRev, NULL); -- _setBegin(qualRev, NULL); -- _setBegin(name, NULL); -+ _setBegin(patFw, (Dna5*)NULL); -+ _setBegin(patRc, (Dna5*)NULL); -+ _setBegin(qual, (char*)NULL); -+ _setBegin(patFwRev, (Dna5*)NULL); -+ _setBegin(patRcRev, (Dna5*)NULL); -+ _setBegin(qualRev, (char*)NULL); -+ _setBegin(name, (char*)NULL); - for(int j = 0; j < 3; j++) { -- _setBegin(altPatFw[j], NULL); -- _setBegin(altPatFwRev[j], NULL); -- _setBegin(altPatRc[j], NULL); -- _setBegin(altPatRcRev[j], NULL); -- _setBegin(altQual[j], NULL); -- _setBegin(altQualRev[j], NULL); -+ _setBegin(altPatFw[j], (Dna5*)NULL); -+ _setBegin(altPatFwRev[j], (Dna5*)NULL); -+ _setBegin(altPatRc[j], (Dna5*)NULL); -+ _setBegin(altPatRcRev[j], (Dna5*)NULL); -+ _setBegin(altQual[j], (char*)NULL); -+ _setBegin(altQualRev[j], (char*)NULL); - } - } - diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch deleted file mode 100644 index 52cb4f496521..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-popcount.patch +++ /dev/null @@ -1,24 +0,0 @@ -Description: Use SeqAn 1.4's seqan::popCount() function instead of own function -Author: Ognyan Kulev -Last-Update: 2014-03-08 ---- -This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -476,6 +476,8 @@ static String getDeltaMap(T v, const - return amap; - } - -+// Debian: Use seqan::popCount -+#if 0 - /** - * Return population count (count of all bits set to 1) of i. - */ -@@ -488,6 +490,7 @@ static unsigned int popCount(T i) { - } - return cnt; - } -+#endif - - /** - * Calculate log-base-2 of i diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch deleted file mode 100644 index 171f9bab8fae..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-ChunkPool.patch +++ /dev/null @@ -1,382 +0,0 @@ -Description: Renamed ChunkPool class to bowtieChunkPool. - SeqAn has a class with the same name and fatal name collision happens. -Forwarded: no -Author: Ognyan Kulev -Last-Update: 2013-04-18 - ---- a/aligner.h -+++ b/aligner.h -@@ -337,7 +337,7 @@ public: - bool verbose, - bool quiet, - int maxBts, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - int *btCnt = NULL, - AlignerMetrics *metrics = NULL) : - Aligner(true, rangeMode), -@@ -544,7 +544,7 @@ protected: - bool quiet_; // don't print informational/warning info - - const int maxBts_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - int *btCnt_; - AlignerMetrics *metrics_; - }; -@@ -585,7 +585,7 @@ public: - bool verbose, - bool quiet, - int maxBts, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - int *btCnt) : - Aligner(true, rangeMode), - refs_(refs), -@@ -1358,7 +1358,7 @@ protected: - bool quiet_; - - int maxBts_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - int *btCnt_; - - // Range-finding state for first mate -@@ -1482,7 +1482,7 @@ public: - bool verbose, - bool quiet, - int maxBts, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - int *btCnt) : - Aligner(true, rangeMode), - refs_(refs), -@@ -2035,7 +2035,7 @@ protected: - TDriver* driver_; - - // Pool for distributing chunks of best-first path descriptor memory -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - - bool verbose_; - bool quiet_; ---- a/aligner_0mm.h -+++ b/aligner_0mm.h -@@ -32,7 +32,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool maqPenalty, -@@ -124,7 +124,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - bool maqPenalty_; -@@ -164,7 +164,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -366,7 +366,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool reportSe_; ---- a/aligner_1mm.h -+++ b/aligner_1mm.h -@@ -32,7 +32,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool maqPenalty, -@@ -161,7 +161,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool maqPenalty_; -@@ -201,7 +201,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -478,7 +478,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool reportSe_; ---- a/aligner_23mm.h -+++ b/aligner_23mm.h -@@ -33,7 +33,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool maqPenalty, -@@ -231,7 +231,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool maqPenalty_; -@@ -273,7 +273,7 @@ public: - RangeCache *cacheFw, - RangeCache *cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -675,7 +675,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool reportSe_; ---- a/aligner_seed_mm.h -+++ b/aligner_seed_mm.h -@@ -37,7 +37,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool maqPenalty, -@@ -554,7 +554,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - bool strandFix_; -@@ -598,7 +598,7 @@ public: - RangeCache* cacheFw, - RangeCache* cacheBw, - uint32_t cacheLimit, -- ChunkPool *pool, -+ bowtieChunkPool *pool, - BitPairReference* refs, - vector >& os, - bool reportSe, -@@ -1375,7 +1375,7 @@ private: - RangeCache *cacheFw_; - RangeCache *cacheBw_; - const uint32_t cacheLimit_; -- ChunkPool *pool_; -+ bowtieChunkPool *pool_; - BitPairReference* refs_; - vector >& os_; - const bool reportSe_; ---- a/ebwt_search.cpp -+++ b/ebwt_search.cpp -@@ -111,7 +111,7 @@ static bool strandFix; // attempt to fi - static bool randomizeQuals; // randomize quality values - static bool stats; // print performance stats - static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread --static int chunkSz; // size of single chunk disbursed by ChunkPool -+static int chunkSz; // size of single chunk disbursed by bowtieChunkPool - static bool chunkVerbose; // have chunk allocator output status messages? - static bool recal; - static int recalMaxCycle; -@@ -223,7 +223,7 @@ static void resetOptions() { - randomizeQuals = false; // randomize quality values - stats = false; // print performance stats - chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread -- chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB) -+ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB) - chunkVerbose = false; // have chunk allocator output status messages? - recal = false; - recalMaxCycle = 64; -@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - UnpairedExactAlignerV1Factory alSEfact( - ebwt, - NULL, -@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat - // Global initialization - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - - Unpaired1mmAlignerV1Factory alSEfact( - ebwtFw, -@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); - -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - Unpaired23mmAlignerV1Factory alSEfact( - ebwtFw, - &ebwtBw, -@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt - // Global initialization - PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); - HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); -- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); -+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose); - - AlignerMetrics *metrics = NULL; - if(stats) { ---- a/ebwt_search_backtrack.h -+++ b/ebwt_search_backtrack.h -@@ -2724,7 +2724,7 @@ public: - bool verbose, - bool quiet, - bool mate1, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt) : - SingleRangeSourceDriver( - params, rs, fw, sink, sinkPt, os, verbose, -@@ -2927,7 +2927,7 @@ public: - bool verbose, - bool quiet, - bool mate1, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt = NULL) : - params_(params), - rs_(rs), -@@ -2986,7 +2986,7 @@ protected: - bool verbose_; - bool quiet_; - bool mate1_; -- ChunkPool* pool_; -+ bowtieChunkPool* pool_; - int *btCnt_; - }; - ---- a/pool.h -+++ b/pool.h -@@ -19,13 +19,13 @@ - * is set at construction time. Heap memory is only allocated at - * construction and deallocated at destruction. - */ --class ChunkPool { -+class bowtieChunkPool { - public: - /** - * Initialize a new pool with an initial size of about 'bytes' - * bytes. Exit with an error message if we can't allocate it. - */ -- ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : -+ bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) : - verbose(verbose_), patid(0), pool_(NULL), cur_(0), - chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz), - bits_(lim_), exhaustCrash_(false), -@@ -38,7 +38,7 @@ public: - } - } catch(std::bad_alloc& e) { - ThreadSafe _ts(&gLock); -- std::cerr << "Error: Could not allocate ChunkPool of " -+ std::cerr << "Error: Could not allocate bowtieChunkPool of " - << totSz << " bytes" << std::endl; - exhausted(); - throw 1; // Exit if we haven't already -@@ -48,7 +48,7 @@ public: - /** - * Delete all the pools. - */ -- ~ChunkPool() { -+ ~bowtieChunkPool() { - if(pool_ != NULL) delete[] pool_; - } - -@@ -189,7 +189,7 @@ public: - * Initialize a new pool with an initial size of about 'bytes' - * bytes. Exit with an error message if we can't allocate it. - */ -- AllocOnlyPool(ChunkPool* pool, const char *name) : -+ AllocOnlyPool(bowtieChunkPool* pool, const char *name) : - pool_(pool), name_(name), curPool_(0), cur_(0) - { - assert(pool != NULL); -@@ -388,7 +388,7 @@ protected: - lastCurInPool_.pop_back(); - } - -- ChunkPool* pool_; -+ bowtieChunkPool* pool_; - const char *name_; - std::vector pools_; /// the memory pools - uint32_t curPool_; /// pool we're current allocating from ---- a/range_source.h -+++ b/range_source.h -@@ -1388,7 +1388,7 @@ class PathManager { - - public: - -- PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : -+ PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) : - branchQ_(verbose, quiet), - cpool(cpool_), - bpool(cpool, "branch"), -@@ -1637,7 +1637,7 @@ protected: - - public: - -- ChunkPool *cpool; // pool for generic chunks of memory -+ bowtieChunkPool *cpool; // pool for generic chunks of memory - AllocOnlyPool bpool; // pool for allocating Branches - AllocOnlyPool rpool; // pool for allocating RangeStates - AllocOnlyPool epool; // pool for allocating Edits -@@ -1811,7 +1811,7 @@ public: - bool quiet, - bool mate1, - uint32_t minCostAdjustment, -- ChunkPool* pool, -+ bowtieChunkPool* pool, - int *btCnt) : - RangeSourceDriver(true, minCostAdjustment), - len_(0), mate1_(mate1), diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch b/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch deleted file mode 100644 index 38664aeee989..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch +++ /dev/null @@ -1,85 +0,0 @@ -Description: Renamed seqan::fill function calls to use seqan::resize. - SeqAn 1.3 renamed seqan::fill() to seqan::resize(). - SeqAn ticket: http://trac.seqan.de/ticket/77 -Forwarded: no -Author: Ognyan Kulev -Last-Update: 2014-08-13 - ---- a/blockwise_sa.h -+++ b/blockwise_sa.h -@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA::buildS - try { - // Allocate and initialize containers for holding bucket - // sizes and representatives. -- fill(bucketSzs, numBuckets, 0, Exact()); -- fill(bucketReps, numBuckets, OFF_MASK, Exact()); -+ resize(bucketSzs, numBuckets, 0, Exact()); -+ resize(bucketReps, numBuckets, OFF_MASK, Exact()); - } catch(bad_alloc &e) { - if(this->_passMemExc) { - throw e; // rethrow immediately -@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA::nextBl - // Not the last bucket - assert_lt(_cur, length(_sampleSuffs)); - hi = _sampleSuffs[_cur]; -- fill(zHi, _dcV, 0, Exact()); -+ resize(zHi, _dcV, 0, Exact()); - assert_eq(zHi[0], 0); - calcZ(t, hi, zHi, this->verbose(), this->sanityCheck()); - } -@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA::nextBl - assert_gt(_cur, 0); - assert_leq(_cur, length(_sampleSuffs)); - lo = _sampleSuffs[_cur-1]; -- fill(zLo, _dcV, 0, Exact()); -+ resize(zLo, _dcV, 0, Exact()); - assert_gt(_dcV, 3); - assert_eq(zLo[0], 0); - calcZ(t, lo, zLo, this->verbose(), this->sanityCheck()); ---- a/diff_sample.h -+++ b/diff_sample.h -@@ -452,7 +452,7 @@ static String getDeltaMap(T v, const - // Declare anchor-map-related items - String amap; - size_t amapEnts = 1; -- fill(amap, v, 0xffffffff, Exact()); -+ resize(amap, v, 0xffffffff, Exact()); - amap[0] = 0; - // Print out difference cover (and optionally calculate - // anchor map) -@@ -532,7 +532,7 @@ public: - assert_gt(_d, 0); - assert_eq(1, popCount(_v)); // must be power of 2 - // Build map from d's to idx's -- fill(_dInv, _v, 0xffffffff, Exact()); -+ resize(_dInv, _v, 0xffffffff, Exact()); - uint32_t lim = (uint32_t)length(_ds); - for(uint32_t i = 0; i < lim; i++) { - _dInv[_ds[i]] = i; -@@ -656,7 +656,7 @@ void DifferenceCoverSample::doBuil - VMSG_NL(" Doing sanity check"); - TIndexOffU added = 0; - String sorted; -- fill(sorted, length(_isaPrime), OFF_MASK, Exact()); -+ resize(sorted, length(_isaPrime), OFF_MASK, Exact()); - for(size_t di = 0; di < this->d(); di++) { - uint32_t d = _ds[di]; - size_t i = 0; -@@ -717,7 +717,7 @@ void DifferenceCoverSample::buildS - assert_eq(length(_doffs), d+1); - // Size sPrime appropriately - reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS -- fill(sPrime, sPrimeSz, OFF_MASK, Exact()); -+ resize(sPrime, sPrimeSz, OFF_MASK, Exact()); - // Slot suffixes from text into sPrime according to the mu - // mapping; where the mapping would leave a blank, insert a 0 - TIndexOffU added = 0; -@@ -823,7 +823,7 @@ void DifferenceCoverSample::build( - // arrays back into sPrime. - VMSG_NL(" Allocating rank array"); - reserve(_isaPrime, length(sPrime)+1, Exact()); -- fill(_isaPrime, length(sPrime), OFF_MASK, Exact()); -+ resize(_isaPrime, length(sPrime), OFF_MASK, Exact()); - assert_gt(length(_isaPrime), 0); - { - Timer timer(cout, " Ranking v-sort output time: ", this->verbose()); diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch deleted file mode 100644 index ff484dfa3ebb..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch +++ /dev/null @@ -1,48 +0,0 @@ -Author: Andreas Tille -Last-Update: Thu, 01 Oct 2015 09:47:23 +0200 -Description: Fix spelling - ---- a/MANUAL -+++ b/MANUAL -@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie - actually wrapper scripts that call binary programs as appropriate. The - wrappers shield users from having to distinguish between "small" and - "large" index formats, discussed briefly in the following section. The --appropiate index type is selected based on the input size. -+appropriate index type is selected based on the input size. - - It is recommended that you always run the bowtie wrappers and not run - the binaries directly. ---- a/MANUAL.markdown -+++ b/MANUAL.markdown -@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie - actually wrapper scripts that call binary programs as appropriate. The - wrappers shield users from having to distinguish between "small" and - "large" index formats, discussed briefly in the following section. The --appropiate index type is selected based on the input size. -+appropriate index type is selected based on the input size. - - It is recommended that you always run the bowtie wrappers and not run - the binaries directly. ---- a/doc/manual.html -+++ b/doc/manual.html -@@ -201,7 +201,7 @@ T2302111203131231130300111123220 -

Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is --ff. This is because most SOLiD datasets have that orientation.

-

Note that SOLiD-generated read files can have "orphaned" mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to .csfastq files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click "NGS: QC and manipulation", then "SOLiD-to-FASTQ" in the left-hand sidebar).

-

Wrapper scripts

--

The bowtie, bowtie-build and bowtie-inspect executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.

-+

The bowtie, bowtie-build and bowtie-inspect executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between "small" and "large" index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.

-

It is recommended that you always run the bowtie wrappers and not run the binaries directly.

-

Small and large indexes

-

bowtie-build can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, bowtie-build builds a "small" index using 32-bit numbers in various parts of the index. When the genome is longer, bowtie-build builds a "large" index using 64-bit numbers. Small indexes are stored in files with the .ebwt extension, and large indexes are stored in files with the .ebwtl extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.

---- a/ref_read.cpp -+++ b/ref_read.cpp -@@ -263,7 +263,7 @@ fastaRefReadSizes(vector& in, - << "reference into smaller chunks and index each independently." << endl; - #else - cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl -- << "build a large index instead using the appropiate options." << endl; -+ << "build a large index instead using the appropriate options." << endl; - #endif - throw 1; - } diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch b/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch deleted file mode 100644 index bc0f1d09557d..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch +++ /dev/null @@ -1,18 +0,0 @@ -Fixes missing tinythread.cpp when using TBB: - -ebwt_search.cpp:(.text+0x91bb): undefined reference to `tthread::thread::join()' - ---- bowtie-1.1.2/Makefile -+++ bowtie-1.1.2/Makefile -@@ -106,10 +106,7 @@ - endif - - OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ -- edit.cpp ebwt.cpp --ifneq (1,$(WITH_TBB)) -- OTHER_CPPS += tinythread.cpp --endif -+ edit.cpp ebwt.cpp tinythread.cpp - - SEARCH_CPPS = qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp \ - log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp \ diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch b/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch deleted file mode 100644 index 54391ae415a3..000000000000 --- a/sci-biology/bowtie/files/bowtie-1.1.2-unbundle-seqan.patch +++ /dev/null @@ -1,27 +0,0 @@ -Description: Use Debian packaged SeqAn library instead of copy in upstream source -Author: Andreas Tille -Date: 2011-01-30 -Last-Update: 2013-04-18 -Reviewed-by: Ognyan Kulev - ---- a/Makefile -+++ b/Makefile -@@ -5,9 +5,7 @@ - prefix = /usr/local - bindir = $(prefix)/bin - --SEQAN_DIR = SeqAn-1.1 --SEQAN_INC = -I $(SEQAN_DIR) --INC = $(SEQAN_INC) -I third_party -+INC = `pkg-config --cflags seqan-1.4` - CPP = g++ - CXX = $(CPP) - CC = gcc -@@ -168,7 +166,6 @@ - $(wildcard genomes/NC_008253.fna) \ - $(wildcard reads/e_coli_1000.*) \ - $(wildcard reads/e_coli_1000_*) \ -- SeqAn-1.1 \ - bowtie \ - bowtie-build \ - bowtie-inspect \ diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest index 634ffefa74ec..742fc01f8c04 100644 --- a/sci-biology/embassy/Manifest +++ b/sci-biology/embassy/Manifest @@ -1,2 +1,2 @@ -EBUILD embassy-6.6.0-r1.ebuild 965 BLAKE2B 736fb94d1774dfa22a0b7b9ea4809389cb65ed1e79ac44b908eb76c0fc348f1ebed4a41dd7c9d19f7b4118509055309f0e0351b8067872c1a461029d96249c10 SHA512 8dd638ed450b83656c3848bd014f2429a9e269f3e3dea5c16e370becbdb1473f2eec261fbfe2b4bc5675262ac6d9ce871fc287045f777a5d0f85a3f05bbf795b +EBUILD embassy-6.6.0-r2.ebuild 929 BLAKE2B 378e0757280f2e0bc04d673892f79ce0139100790e84618697c4e55d23f4bcb193c075cca1a5ca9aa67eacb0412250be1186e3b32eeff28306358b753852e32d SHA512 1f17adca5f631bea36776135ae545411a35f3d575eb4e059bde004fa3616447ee3eb5f1b867c5c4debfc95a5d6d476b3d2c1a80b2a8bb429c3ce4db83b0f1e4d MISC metadata.xml 347 BLAKE2B 2368d452e759747738601ae0e5e5e7181167badeaa28ed89aa8e07b55ebc9d2f1dbcd351cd5569a4548c307cfaa23b26756d88778c078685848db72dd9b094e7 SHA512 d6ddcfb5e3234d23f3c500a7234b0bc77ecdb0cf52f35f041ffdd444b8b3fefe7d0b3e89e5f7fb86da375647b7436ab1766b5bff186206e189045e38ade2056e diff --git a/sci-biology/embassy/embassy-6.6.0-r1.ebuild b/sci-biology/embassy/embassy-6.6.0-r1.ebuild deleted file mode 100644 index b30223eda805..000000000000 --- a/sci-biology/embassy/embassy-6.6.0-r1.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" -HOMEPAGE="http://emboss.sourceforge.net/embassy/" - -LICENSE="metapackage" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~x86-linux" - -RDEPEND=" - >=sci-biology/embassy-cbstools-1.0.0.660 - >=sci-biology/embassy-clustalomega-1.1.0.660 - >=sci-biology/embassy-domainatrix-0.1.660 - >=sci-biology/embassy-domalign-0.1.660 - >=sci-biology/embassy-domsearch-0.1.660 - >=sci-biology/embassy-emnu-1.05.660 - >=sci-biology/embassy-esim4-1.0.0.660 - >=sci-biology/embassy-hmmer-2.3.2.660 - >=sci-biology/embassy-iprscan-4.3.1.660 - >=sci-biology/embassy-meme-4.7.660 - >=sci-biology/embassy-mse-3.0.0.660 - >=sci-biology/embassy-phylipnew-3.69.660 - >=sci-biology/embassy-signature-0.1.660 - >=sci-biology/embassy-structure-0.1.660 - >=sci-biology/embassy-topo-2.0.660 - >=sci-biology/embassy-vienna-1.7.2.660 -" diff --git a/sci-biology/embassy/embassy-6.6.0-r2.ebuild b/sci-biology/embassy/embassy-6.6.0-r2.ebuild new file mode 100644 index 000000000000..c0777d1aac70 --- /dev/null +++ b/sci-biology/embassy/embassy-6.6.0-r2.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" +HOMEPAGE="http://emboss.sourceforge.net/embassy/" + +LICENSE="metapackage" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x86-linux" + +RDEPEND=" + >=sci-biology/embassy-cbstools-1.0.0.660 + >=sci-biology/embassy-clustalomega-1.1.0.660 + >=sci-biology/embassy-domainatrix-0.1.660 + >=sci-biology/embassy-domalign-0.1.660 + >=sci-biology/embassy-domsearch-0.1.660 + >=sci-biology/embassy-emnu-1.05.660 + >=sci-biology/embassy-esim4-1.0.0.660 + >=sci-biology/embassy-hmmer-2.3.2.660 + >=sci-biology/embassy-iprscan-4.3.1.660 + >=sci-biology/embassy-mse-3.0.0.660 + >=sci-biology/embassy-phylipnew-3.69.660 + >=sci-biology/embassy-signature-0.1.660 + >=sci-biology/embassy-structure-0.1.660 + >=sci-biology/embassy-topo-2.0.660 + >=sci-biology/embassy-vienna-1.7.2.660 +" diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest index edfda5895233..1ffc0cd9c93a 100644 --- a/sci-biology/exonerate/Manifest +++ b/sci-biology/exonerate/Manifest @@ -1,4 +1,4 @@ AUX exonerate-2.2.0-asneeded.patch 362 BLAKE2B 57bb7d7d57bf2347fc0cb20f650cd0a452bd70ed8ed46a87d132cf8d68e152438ec2c4e877129feb91748f5ca43021cc0010cf2f50b3bdb8eed60218d904eb27 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c EBUILD exonerate-2.2.0-r2.ebuild 967 BLAKE2B 27a48f5dc4e1040f4296152ae445ba6bb2dc29132605b6cce240c40d2719d16c0c7d80103d2b9f8440fb7d5bb8fec3e8ba0385f6f87b9196b443dd14ae1a6310 SHA512 1d5be70396afabf08489501cba460bb47a7bfe9efead75226b07707ed00813f0dcd69611b75e3135444ee100ceeaf2cd492cd79ffc5f3d01e6f5d808ce84f2e1 -MISC metadata.xml 438 BLAKE2B ae3dbc6cf8628225e3238076ec24fbadffd60818cb051cfc153c37af4cadbce7070697f0a2f21219a5a32aa9ebe8e4518fb2e4eb0e147959965f468fb0629b2d SHA512 e77d02d4d9664234895ef29ffc633e2e8ae49ac8c324fe0e82ac6ec3ac416570443f4a9831838d2eceb420398dfb5c5872b562861002974fa8754b2d846cf777 +MISC metadata.xml 326 BLAKE2B 51316d3ba2a93eeda2dc044ff76245b49ab71781bd822dbd52e790c738e866c899b4efd47daf298a6cad7258091ee1163778fae39c7cd27cf5a64408dc559d39 SHA512 226349d3fc3368937b974630a4251d2f6ac067a92325a376c278570beca0d316c8749e7026bd6d337f7c1cf9abd9d760499e6a7d8d85f00822a10575978e8973 diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml index 7851377e083e..b64950792715 100644 --- a/sci-biology/exonerate/metadata.xml +++ b/sci-biology/exonerate/metadata.xml @@ -5,9 +5,6 @@ sci-biology@gentoo.org Gentoo Biology Project - - exonerate is a generic tool for pairwise sequence comparison - Install all utilities diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest index 385708b89211..1eb48ad0f1f3 100644 --- a/sci-biology/finchtv/Manifest +++ b/sci-biology/finchtv/Manifest @@ -1,4 +1,4 @@ DIST finchtv_1_3_1.tar.gz 6706911 BLAKE2B 5aea60c2a107dc0d1d878b0416011f57bfcdb73b6e7c0da80be5b485ec5824aae7c610235057b74002765f5ab5e7bd250efec2a04a471b55abd046afc560ea38 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8 EBUILD finchtv-1.3.1-r2.ebuild 610 BLAKE2B 4c58fdc546782232ea8c1fc5937ab83ba36000bbea56b83d813a9afd52cdc9caff0b946235f9d452c2ee287d11a228697c8a972e2bbbdaa94c640e4ac40c82eb SHA512 693cc060e91d2ed1ca9d4bc6ff6baaa9a3afe1a876d83d79e3cc3d4c416f8e7ddc878696e890e0b4e660ed5c017c0402bb8247e1b4d6d819f567292b5aa168a7 EBUILD finchtv-1.3.1-r3.ebuild 694 BLAKE2B ede749140addd096bd6ab449b94af6f204b8970b4978d49971ff1c46d3cde1bd225a8792ea76b68272ca080ac08b8d989e8cf704b09797b3b5d5bad0ec0c47e3 SHA512 0772745c5d1d529def77475c8fdc90321c029dbd0b87ea5b65db65cf29485a8e59b2c0aa2003e6c8d0b7b2bffdb5b988d1452da7a7d32775b539dd2676f59a96 -MISC metadata.xml 374 BLAKE2B 1aeffa98b6c6a1ebf19451781a691992a8662bb1de184ab26bac1455d3dbd5ea182f7a7d44b8dd7b943dd400af365f70ee0693921a5216783f201078e61157f3 SHA512 5e1e1540a94ba73446163db04367641e83cc222dec5e062ff8159b9a16a256729fecf19ee19c9980a2a88da6b39e4d21334d7bbba8526c34e05d22c1e578b16d +MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml index a46ebf47e871..959160fe46b1 100644 --- a/sci-biology/finchtv/metadata.xml +++ b/sci-biology/finchtv/metadata.xml @@ -5,7 +5,4 @@ sci-biology@gentoo.org Gentoo Biology Project - -A cross-platform graphical viewer for chromatogram files. - diff --git a/sci-biology/libgtextutils/Manifest b/sci-biology/libgtextutils/Manifest index dc3c8bb842ae..74b2ae8850e5 100644 --- a/sci-biology/libgtextutils/Manifest +++ b/sci-biology/libgtextutils/Manifest @@ -2,4 +2,4 @@ AUX libgtextutils-0.6.1-fix-build-system.patch 1719 BLAKE2B 993f1e68f960853a264d AUX libgtextutils-0.6.1-gcc6.patch 724 BLAKE2B 14ebd0ab5ec4685688caa922dacccdaad9101af0814a93b08f0c9ba5e50ac6a02291528b6ad3d61b48a2f29a25b63e421690f19109351f4472cc118886ca0e10 SHA512 74ec8fafc699cadc5d40f5284cd42cfb8c949744b7a16bbf8142c8db71ad6c921551da03f260e82bfe84b69dd5fbd2261031fe22aee6b3396515b1f66576a530 DIST libgtextutils-0.6.1.tar.bz2 273459 BLAKE2B 81b1e9b467287ed9551fc53abddf5757efb2dd1c98f0388e2128535fbe70b706badd5702a5b5c3cb19a34c26ffa218c9c41caf9f17770a015b09fc13fabe4d53 SHA512 0bc392385f9e6c345dff82b3fb04f322e8aceca769e15a3a87da6c718b6e9a7e1de082940d4bb0339a4c3a86f706fde0de047df459682aa9ea216d6e5c17eab6 EBUILD libgtextutils-0.6.1.ebuild 623 BLAKE2B 5bd2ff34a6898b662e6e624a77682a358b9340c6b94b9dfa40bec0637d4074ec648ca6146ee870f9cf5a8141028d23aedc55407aea04fbf2b69d62699d69d547 SHA512 e72eaddb48422afe71140394825964e6778a339ea182d614178061eb294dada1b81e7b5221a1a19d9d2ac720200f6eb4a7eab09f6ef1b7425ce7dda491add449 -MISC metadata.xml 379 BLAKE2B b5f42185a237d0dd1dcbf6c5ae9e007f0a2f875ab0e7c4e6bb8cca07b6f24248d449541e0f455687a0876d7286bc8fbd08e72df88cffc69d255d22788fbadc05 SHA512 9b77656bd047462678494259c168f2214238c909e4dd19ff822cf182e442ce385a3375158fcc0a1be53303a4828e6339ea379f9de60851c894b8d57c0a099aea +MISC metadata.xml 370 BLAKE2B 01c5f6253c80b7fc48e8c7980c62366fd38643da25fdd999cef041558b7d559cb45a22a6125d222569104443c75045e6169f133bc46871ab9f567bdf3f3ae3dc SHA512 b9a044abc657680f9c8fdc80d318b5a9891c5c532eb0831f00bf2f774391c885cf568f6ec3376617da2a5d4d8f9b87283384d595086b3ae57defbc988e96f1c1 diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml index 138cb7705c0a..38108be67e14 100644 --- a/sci-biology/libgtextutils/metadata.xml +++ b/sci-biology/libgtextutils/metadata.xml @@ -2,7 +2,7 @@ - mmokrejs@fold.natur.cuni.cz + mmokrejs@gmail.com Martin Mokrejs diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index 12365d2c556e..5ce9c67f4212 100644 --- a/sci-biology/seqan/Manifest +++ b/sci-biology/seqan/Manifest @@ -1,13 +1,6 @@ -AUX seqan-1.4.2-buildsystem.patch 870 BLAKE2B 2b3e32e4bea47caf6165e1c0ab89cdadf1e4d4756bb3ddd77b943b89a9366fb28d49dfdc22d69d5c431f78a83fc73b20c486085804a153c987020b3e28120b20 SHA512 d769eb4137c8c0ddb7137ecfdb0673ba8648ae720673848cbb473a0c80d479b6e5c564c12f1a9dd01953d955605eb2f273e04808ae50058c565e997381c3f748 -AUX seqan-1.4.2-include.patch 552 BLAKE2B f8d67014e59751616227471995254684b3edfacacfb455099f99c719f5602c88f0d106df01354921557d3324f77e03934606f698801516bc8432837c6211b67e SHA512 b02ab4fe49a511494134e44855d865f0ff210392810970834deb304499b5017764ed1c04d8f8dbfb513c333ac302946e5c72c9160cd38a5ef5ad095a865cb6d0 -AUX seqan-1.4.2-shared.patch 974 BLAKE2B e46b6b61c4927ca36c53e68e39c77eb5d983221dd074040a8911a7d7dfb04d2fb4c4ded0f3c9b6d90082a26f704654daa1d2b70e547b9ad657cc48bb96fc435b SHA512 a509c243244b6b40b26700a73be267558ceb17c4e0079f3eca606835ecfe8d1417b88fd37719ca9cf226e6d2d33ee3e22790b20e39a86a300f722eb186cabaad AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3fc76141320f5a71cfd0fe102b8e511ccb36d48e021baf0928ac8857e97f6addde3f15f4f0577c531285027f23f5eea8 SHA512 f8a3df0892a81a65562dbd85f0945e5722df524e07b9949f860df4e0f07c285df3a48a112c8e1e5dca28a97c219dc9feed677e803ec5d3964216f7052b6f431b AUX seqan.pc.in 263 BLAKE2B ffd2a2c1ac74af7bc6b33c5959792551447ee61fe87fbb8bc6966ad44c33ae5bd512e836bc67175a3bf1895554364e48fcfea207f94f18ef72b7eae74fbe82d5 SHA512 bde1c89624284a37dac1a8717049a3b14340a2543003d9cf8406bddf4033541b65b617b802b18c80b2c7733d55ad9d7484bd85fdc927582363885da6d0210af7 -DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a -DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b -EBUILD seqan-1.4.2-r1.ebuild 1997 BLAKE2B 7e7934e70e17b65cc3557dc2f9e7c7d16db4f57bee1b0238d211ed57039e47cc03f495dc068e94d5d4502983c0d0e3b4cca21c0e88ff6c63a9e4d1496ba2850d SHA512 b1ba7611fe3de91484b05e06e4313eb7422bf38d5987c164e9ae7b788b4e7c3cdc0cd5702c215bd6747d2dd94f305f9ae8ea359699e5c32114e8a03514007bfd -EBUILD seqan-2.2.0-r1.ebuild 2703 BLAKE2B e56cdb3ad4cf674e2349a8d380b49c58b68b528ae28e7b52066a24cf09efbc262855d51f8f3a6ae8111e46b3f95bcec8eaa117a43a895c5bca59963769300307 SHA512 e9524b59db85d13554f99b01c681e2d9137d8971a7df628c2a0b7f5774f8ea324191b3ed6bf0c51b8023b7b1947586adad22709c959656cf1fda58c92c3d89a6 -EBUILD seqan-2.4.0.ebuild 1917 BLAKE2B c53b1c51fd7b8a1c1498f5b2072f26a7829545f626fef177e0e64bc488784f7b9273c2f101db4c045203b3198aa6f37fa6f3226c633575815fbb95174ed5d30a SHA512 6f17b5d2d3be7a19fadcad798f0328fe467bc811d0a931c7b43df87fe23d17ebf2fb48aa197b838c9756bf9f3af7eaa04d346b0b5a05b03b28d03e4e80400c71 -EBUILD seqan-9999.ebuild 1860 BLAKE2B 745e69b7a80868f3faf45a6dfc9727835c8482737b3902a9e0f809a456ce5b3335d821d1106579da01fa495bc3df1caf222f425e41e172479b7de4e4a6e6a2b4 SHA512 3da317388c84933b817705825385c20c3673208c9a3fa1867078f7aea6a9959c6db3b8463cc3713d728180e30093cb1e30220072866305ac58f7b3de6b412f83 +EBUILD seqan-2.4.0.ebuild 1624 BLAKE2B e2b8d8c2e7f87abc063255e0c6c826a57e4da29b063eb3fc82d143593e06d8cbbf5744cd6e39e9cc1b2623c010d181e4361665946a8489ad454f3e1fb9a33c88 SHA512 1d39216baa3877df91b19f36519103114a6858b4600d5bfe3ba01e5619bcfb2543d208e7d5af2806a5c964ebcb8399a8244ca65f4e7ecf169e02827e055545d3 +EBUILD seqan-9999.ebuild 1567 BLAKE2B b171570acf62243121541b771c26fd7ef86e4be86878c060050af2cd665973182e2498f9ba9c336e8a382768b71aa3547edde927682dcdd844c6fd0ed9e2cd99 SHA512 b91b532d3655de47c0cfb9f243e46c120d5259f9166be4e41d7b0dd02a6f681e714fd5941aadb54b6ee89a0f5a4aa10628157c9b25bfd8074178dc36b70e5944 MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17 diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch deleted file mode 100644 index 4c7893e90c05..000000000000 --- a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch +++ /dev/null @@ -1,30 +0,0 @@ -Add default disabled flag to enable generation of documentation. -For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a -support library for legacy tools. - ---- seqan-1.4.2/CMakeLists.txt -+++ seqan-1.4.2/CMakeLists.txt -@@ -123,10 +123,12 @@ - add_subdirectory (core) - message (STATUS "Configuring extras") - add_subdirectory (extras) -+if (NOT SEQAN_NO_DOX) - message (STATUS "Configuring docs") - add_subdirectory (docs) - message (STATUS "Configuring manual") - add_subdirectory (manual) -+endif () - message (STATUS "Configuring sandbox") - add_subdirectory (sandbox) - message (STATUS "Configuring util/py_lib") ---- seqan-1.4.2/docs/main.py -+++ seqan-1.4.2/docs/main.py -@@ -123,7 +123,7 @@ - - # Done, print end message. - print 'Documentation created/updated.' -- return dddoc_html.WARNING_COUNT > 0 -+ return 0 - - - def main(argv): diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch deleted file mode 100644 index 5baee4d8ebc0..000000000000 --- a/sci-biology/seqan/files/seqan-1.4.2-include.patch +++ /dev/null @@ -1,16 +0,0 @@ - core/include/seqan/index/index_qgram_openaddressing.h | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h -index 4a6c2e6..8cc9a42 100644 ---- a/core/include/seqan/index/index_qgram_openaddressing.h -+++ b/core/include/seqan/index/index_qgram_openaddressing.h -@@ -35,6 +35,8 @@ - #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H - #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H - -+#include -+ - namespace SEQAN_NAMESPACE_MAIN - { - diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch deleted file mode 100644 index 0f438ff07bce..000000000000 --- a/sci-biology/seqan/files/seqan-1.4.2-shared.patch +++ /dev/null @@ -1,22 +0,0 @@ - util/cmake/SeqAnBuildSystem.cmake | 8 ++++---- - 1 file changed, 4 insertions(+), 4 deletions(-) - -diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake -index bcba2c0..d53cd01 100644 ---- a/util/cmake/SeqAnBuildSystem.cmake -+++ b/util/cmake/SeqAnBuildSystem.cmake -@@ -144,10 +144,10 @@ macro (seqan_register_apps) - set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1") - - # enable static linkage for seqan apps -- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) -- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") -- endif () -+# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) -+# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -+# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") -+# endif () - - # Get all direct entries of the current source directory into ENTRIES. - file (GLOB ENTRIES diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild deleted file mode 100644 index 3a7f55c710c3..000000000000 --- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-any-r1 versionator - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" -SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" - -SLOT="$(get_version_component_range 1-2)" -LICENSE="BSD GPL-3" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="cpu_flags_x86_sse4_1 test" -RESTRICT="!test? ( test )" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2 - sys-libs/zlib" -DEPEND=" - ${RDEPEND} - test? ( - $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -PATCHES=( - "${FILESDIR}/${P}-shared.patch" - "${FILESDIR}/${P}-include.patch" - "${FILESDIR}/${P}-buildsystem.patch" -) - -pkg_setup() { - use test && python-any-r1_pkg_setup -} - -src_prepare() { - # pkg-config file, taken from seqan 2.1 - cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die - sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \ - -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \ - -e "s#@CMAKE_PROJECT_NAME@#${PN}#" \ - -e "s#@SEQAN_VERSION_STRING@#${PV}#" \ - -i ${PN}-${SLOT}.pc || die - - rm -f util/cmake/FindZLIB.cmake || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBoost_NO_BOOST_CMAKE=ON - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=ON - ) - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - # SLOT header such that different seqan versions can be used in parallel - mkdir "${ED}"/usr/include/${PN}-${SLOT} || die - mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die - - # pkg-config file - insinto /usr/share/pkgconfig/ - doins ${PN}-${SLOT}.pc -} - -pkg_postinst() { - einfo "${CATEGORY}/${PF} is only intended as support library for older" - einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop" - einfo "any new software against the latest SeqAn release and not this one." -} diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild deleted file mode 100644 index 5e139cd7e601..000000000000 --- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild +++ /dev/null @@ -1,94 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-any-r1 versionator - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" -SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" - -SLOT="0" -LICENSE="BSD GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cpu_flags_x86_sse4_1 doc test" -RESTRICT="!test? ( test )" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2 - sys-libs/zlib - !!sci-biology/seqan:2.0 - !!sci-biology/seqan:2.1 - !!sci-biology/seqan:2.2" -DEPEND=" - ${RDEPEND} - doc? ( - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - ) - test? ( - $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -S="${WORKDIR}"/${PN}-${PN}-v${PV} - -pkg_setup() { - if use test || use doc; then - python-any-r1_pkg_setup - fi -} - -src_prepare() { - seqan_major_ver=$(get_version_component_range 1) - seqan_majorminor_ver=$(get_version_component_range 1-2) - - # install docs in proper Gentoo structure - sed -e "s#share/doc/seqan#share/doc/${PF}#" \ - -e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \ - -i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die - - # cmake module - sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \ - -e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \ - -e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${seqan_majorminor_ver})#" \ - -i util/cmake/FindSeqAn.cmake || die - - # pkg-config file - sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \ - -i util/pkgconfig/${PN}.pc.in || die - - rm -f util/cmake/FindZLIB.cmake || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=$(usex !doc) - ) - cmake-utils_src_configure -} - -src_compile() { - cmake-utils_src_compile - use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox -} - -src_install() { - cmake-utils_src_install - - # multi-version header such that different seqan versions can be installed in parallel - mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die - mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die - - # pkg-config file - mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die - - # create pkg-config symlink to restore default behaviour - dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc -} diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild index 8b337e77e6be..5653a1ec94e4 100644 --- a/sci-biology/seqan/seqan-2.4.0.ebuild +++ b/sci-biology/seqan/seqan-2.4.0.ebuild @@ -1,12 +1,11 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 : ${CMAKE_MAKEFILE_GENERATOR:=ninja} -PYTHON_COMPAT=( python2_7 ) -inherit cmake-utils multibuild python-any-r1 toolchain-funcs +inherit cmake-utils multibuild toolchain-funcs DESCRIPTION="C++ Sequence Analysis Library" HOMEPAGE="http://www.seqan.de/" @@ -24,7 +23,7 @@ fi LICENSE="BSD GPL-3" SLOT="0" -IUSE="cpu_flags_x86_sse4_1 doc tools" +IUSE="cpu_flags_x86_sse4_1 tools" REQUIRED_USE="cpu_flags_x86_sse4_1" RDEPEND=" @@ -34,21 +33,12 @@ RDEPEND=" !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2" DEPEND=" - ${RDEPEND} - doc? ( - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" + ${RDEPEND}" PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch ) -python_check_deps() { - use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]" -} - pkg_setup() { if [[ ${MERGE_TYPE} != binary ]]; then - use doc && python-any-r1_pkg_setup use tools && tc-check-openmp MULTIBUILD_VARIANTS=( @@ -60,18 +50,19 @@ pkg_setup() { src_configure() { my_configure() { - local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" ) + local mycmakeargs=( + -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" + -DSEQAN_NO_DOX=ON + ) case "${MULTIBUILD_ID}" in tools) mycmakeargs+=( -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS - -DSEQAN_NO_DOX=ON ) ;; library) mycmakeargs+=( -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=$(usex !doc) ) ;; *) diff --git a/sci-biology/seqan/seqan-9999.ebuild b/sci-biology/seqan/seqan-9999.ebuild index 0005819ff4d3..b344b39cbc46 100644 --- a/sci-biology/seqan/seqan-9999.ebuild +++ b/sci-biology/seqan/seqan-9999.ebuild @@ -1,12 +1,11 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 : ${CMAKE_MAKEFILE_GENERATOR:=ninja} -PYTHON_COMPAT=( python2_7 ) -inherit cmake-utils multibuild python-any-r1 toolchain-funcs +inherit cmake-utils multibuild toolchain-funcs DESCRIPTION="C++ Sequence Analysis Library" HOMEPAGE="http://www.seqan.de/" @@ -24,7 +23,7 @@ fi LICENSE="BSD GPL-3" SLOT="0" -IUSE="cpu_flags_x86_sse4_1 doc tools" +IUSE="cpu_flags_x86_sse4_1 tools" REQUIRED_USE="cpu_flags_x86_sse4_1" RDEPEND=" @@ -34,19 +33,10 @@ RDEPEND=" !!sci-biology/seqan:2.1 !!sci-biology/seqan:2.2" DEPEND=" - ${RDEPEND} - doc? ( - $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') - ${PYTHON_DEPS} - )" - -python_check_deps() { - use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]" -} + ${RDEPEND}" pkg_setup() { if [[ ${MERGE_TYPE} != binary ]]; then - use doc && python-any-r1_pkg_setup use tools && tc-check-openmp MULTIBUILD_VARIANTS=( @@ -58,18 +48,19 @@ pkg_setup() { src_configure() { my_configure() { - local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" ) + local mycmakeargs=( + -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" + -DSEQAN_NO_DOX=ON + ) case "${MULTIBUILD_ID}" in tools) mycmakeargs+=( -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS - -DSEQAN_NO_DOX=ON ) ;; library) mycmakeargs+=( -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - -DSEQAN_NO_DOX=$(usex !doc) ) ;; *) -- cgit v1.2.3