diff options
| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-10-16 19:47:08 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-10-16 19:47:08 +0200 |
| commit | f7eaea4317cca5c6ca5566c05c69b604d7312bc8 (patch) | |
| tree | 282ce6f13ef5b285d0ea58c8bd6c8b3e0323b502 | |
| parent | sci-libs/ciftilib: new ebuild (diff) | |
| download | sci-f7eaea43.tar.gz sci-f7eaea43.tar.bz2 sci-f7eaea43.zip | |
sci-biology/SPAdes: version bump, drop old and buggy version
SPAdes 3.13.0
CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected
automatically based on read length.
CHANGE: Added manual as README.md in markdown format for github.
FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.
FIX: Assert for path.length() > 0 in rnaSPAdes.
FIX: CQF and k-mer counting.
REMOVE: dipSPAdes module.
Package-Manager: Portage-2.3.51, Repoman-2.3.10
| -rw-r--r-- | sci-biology/SPAdes/Manifest | 11 | ||||
| -rw-r--r-- | sci-biology/SPAdes/SPAdes-3.13.0.ebuild (renamed from sci-biology/SPAdes/SPAdes-3.12.0.ebuild) | 1 |
2 files changed, 5 insertions, 7 deletions
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index 8945f9f4f..fba8980d4 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -1,6 +1,5 @@ -DIST SPAdes-3.12.0.tar.gz 8681834 BLAKE2B 1e2dd4514d837b49ae475acbe75937e150904c0e124caa02e102eb8164ca0f0ece47517549fbc926c118974c700c82b961150f5a84cd7bc508c02aba490f60e5 SHA512 030ecbfc13cdd4ed2ae9cd360aef1fd8eb36911c47041f981c36a63b8b28b4ec8c030286869df1d231be45f333ef9d39256d1606caf0826739dc022eaeb09512 -DIST SPAdes-3.12.0_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d728aa9df9398ffd8545777dc2d5a69cab4396e73825e4e8f42d3d590cf82ec4f6cbb0e4783d3d731b6637b0ce8cf8afe2ebe689b SHA512 618284c899b5c0f167b91638ac3ca4d7ee2c932f5acbfa6225f43276b073259000022f12afa3d8df26dfd967085b3d2d11ca006766169199afc02de111a78db4 -DIST SPAdes-3.12.0_manual.html 64024 BLAKE2B 4289d36ec221308d04db3d5220890907bccb9d8bd66c839857970f0f36fdbb9c6b9f7cfa6f2fcb83a933784d2b9a82d3507d72be7ac77444e3a81288bf3e21f5 SHA512 00073510a91338586b5b49320bccddf8f078bbd263848e9aa2c690ce7834f4121d708ca06e55fe2a60d43244cfd09d430ebbdcc2997b98b8d51a6d94cf563d98 -DIST SPAdes-3.12.0_manual.md 51253 BLAKE2B 32acdf87e3825959296f91f86bcc7fd12189b920d251f79272d3888fd278bb350958419672d3d788e3dfd3199eed3d9ad3cbaafaf4cf277843621f64fd4d9a1f SHA512 c69cc431c1da6185f1d3ed4c83dc2f63b9ecf724e11a6b65738e0c05103a09afc6ca7185c09b5a7389103a988d2da412b8e91a6e2c663255da5cb48df6d31ebf -DIST SPAdes-3.12.0_rnaspades_manual.html 6408 BLAKE2B 90cd5b7f5624a9edfb8d584288aa4c2d4d71fa8f704308e33549776931647c0c1ed640bb21159f036255e7fa43c8f77292b4396bd6858758f871859eceaab13a SHA512 39acd4ce301708b67201d04c9ae3f994c196914a849e030f736b318aa3b38af3a50a452e467e7496c8a5402d69d17ceffd245e2bde6eb2bb769dc8e780c9e442 -DIST SPAdes-3.12.0_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b +DIST SPAdes-3.13.0.tar.gz 8634070 BLAKE2B 8876c1ebfb7dd6485f5511a6b8b171b05eeb086ac610371833d4f9d24a175d44b7b96fdac010f5ef5ccb63bd9a839c4f83c7c2e1699b5f9239cff5dff28572b2 SHA512 2df8173debad0edb845302dc8e1fed0b459d247c4cb2d92d711ed05e5a1a2bfbb19f97aeec3aab4e991593bc90ba445347cf7e7d528147f76044a5e7f564af10 +DIST SPAdes-3.13.0_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d728aa9df9398ffd8545777dc2d5a69cab4396e73825e4e8f42d3d590cf82ec4f6cbb0e4783d3d731b6637b0ce8cf8afe2ebe689b SHA512 618284c899b5c0f167b91638ac3ca4d7ee2c932f5acbfa6225f43276b073259000022f12afa3d8df26dfd967085b3d2d11ca006766169199afc02de111a78db4 +DIST SPAdes-3.13.0_manual.html 64051 BLAKE2B 6217855724637fd7615d194747fcec6a94f259e3534c52574183d8bcb9cc2bf75435989f75e77774b19d6268aa6eeeb525db8ee305d02419480e285637db971a SHA512 4c80ec091ca3478e26c911313465a886c7768f87574b69a651e7e1519eef73e2bdf147e2d4136993fd309802c0fc9380ffff9a05f2da3aec5db69bbf7cd3af75 +DIST SPAdes-3.13.0_rnaspades_manual.html 7109 BLAKE2B c560e781b97899b02abf1324506a505fafa8819dd2dcf33a60886b19ddb4af515901d3ee4ac98a0d9aa21939e1afa040b0063b287f46b9b02202d5a562ba28b4 SHA512 26761374a6baa706139c108e2695ec56aef8aa1433c72e20b8b73a5e8204a225a9b1e79fddb4f627196005c7e843be8df4a7cd02a653cc47f3a9f8934d96160f +DIST SPAdes-3.13.0_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b diff --git a/sci-biology/SPAdes/SPAdes-3.12.0.ebuild b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild index b56180a1a..00ccc4f27 100644 --- a/sci-biology/SPAdes/SPAdes-3.12.0.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild @@ -12,7 +12,6 @@ HOMEPAGE="http://cab.spbu.ru/software/spades" SRC_URI=" https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html - http://cab.spbu.ru/files/release${PV}/manual.md -> ${P}_manual.md http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html -> ${P}_dipspades_manual.html" |