diff options
Diffstat (limited to 'sci-biology/pufferfish')
| -rw-r--r-- | sci-biology/pufferfish/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch | 31 | ||||
| -rw-r--r-- | sci-biology/pufferfish/metadata.xml | 11 | ||||
| -rw-r--r-- | sci-biology/pufferfish/pufferfish-1.4.0.ebuild | 35 |
4 files changed, 0 insertions, 81 deletions
diff --git a/sci-biology/pufferfish/Manifest b/sci-biology/pufferfish/Manifest deleted file mode 100644 index 4ca8429dc..000000000 --- a/sci-biology/pufferfish/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST htslib-pufferfish-1.4.0.tar.gz 1262620 BLAKE2B 7fff233fadd4737e416058a24d9dc916e5ecf1fa10c456cfb15001df7c664daedecdbcef49469dffb6516c47e00937cbe399a68032fcf18ab9070768d40d3091 SHA512 52ae9099ddadb1d0136f1a62825ff0539baf754302c735ea81b8748a1c349107766b2022cc59814728d366b6df2c9f1b93edf926c1a6a7af78a4f40c4e821c4c -DIST pufferfish-1.4.0.tar.gz 3099274 BLAKE2B 65c26b02513840b3f7b6f381af674b59a21960fe56559b8d87dd22051fa02e7e5c06ab1ba1b9f81516f9831ea1b79492a9cc0e2d0b9258d9c21ddfb7ea162d69 SHA512 683bad5a5e3512c56c211af1270ea1e627d2483d601d20ef70f92087b37327463b36224eda38699231f8daa8c318d745757eed2a4190351ebb8b4a252fca6474 -DIST seqlib-pufferfish-1.4.0.tar.gz 315441 BLAKE2B b402f94837aeb43e4d443044c65d1c193ce7b24a8507b9a79da6cbfc5d7093d286ccd8573eca64c78bd3c65830dc11a18ec26dc619e7ab95d04a472c15ec70d7 SHA512 b3efa0511df9c39ed8021c1bf316f88fb6b51ebd745b7f799bc92edebf31ff7dbd466b83ba30a3381e411d36455f4074163267d4331c5fe16f2934762865d22f -DIST setcover-pufferfish-1.4.0.tar.gz 33911 BLAKE2B 690cfca7e271490ef8b7119fe9fb7df3e7c06897eab52346b485c22a8a7b8e75d344a07f24dbf44aa68919793f942c8f5d1bd1932d2ce1a21a18631e3e64aecf SHA512 8954b38a183f81fff36663c6cbbef25fbf003045d93462933d09f0384f6e17fa726d48e9d94daa5195052e6ff9650aba4a2c8a6f0691f50c360462f02760e2a1 diff --git a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch deleted file mode 100644 index c86fe847f..000000000 --- a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 7f1516a..90f7cdd 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -282,12 +282,9 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}") - - - ExternalProject_Add(libseqlib --GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git --GIT_TAG master - UPDATE_COMMAND "" - UPDATE_DISCONNECTED 1 - BUILD_IN_SOURCE TRUE --DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND ./configure -@@ -300,13 +297,10 @@ INSTALL_COMMAND mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include & - ) - - ExternalProject_Add(libSetCover -- GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git -- GIT_TAG master - UPDATE_COMMAND "" - CONFIGURE_COMMAND "" - UPDATE_DISCONNECTED 1 - BUILD_IN_SOURCE TRUE -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - BUILD_COMMAND make -j8 diff --git a/sci-biology/pufferfish/metadata.xml b/sci-biology/pufferfish/metadata.xml deleted file mode 100644 index 7b582e896..000000000 --- a/sci-biology/pufferfish/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">COMBINE-lab/pufferfish</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild deleted file mode 100644 index 588970e06..000000000 --- a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -SC_COMMIT="b1de7919c0a4d0e65c5cd0b6d78963516e44be25" -SL_COMMIT="340dad36dff67ca96815bd412fe65587d4d64479" -HL_COMMIT="be22a2a1082f6e570718439b9ace2db17a609eae" - -DESCRIPTION="Index for the colored, compacted, de Bruijn graph" -HOMEPAGE="https://github.com/COMBINE-lab/pufferfish" -SRC_URI="https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/martin-steinegger/setcover/archive/${SC_COMMIT}.tar.gz -> setcover-${P}.tar.gz - https://github.com/COMBINE-lab/SeqLib/archive/${SL_COMMIT}.tar.gz -> seqlib-${P}.tar.gz - https://github.com/samtools/htslib/archive/${HL_COMMIT}.tar.gz -> htslib-${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -DEPEND="dev-cpp/tbb" - -S="${WORKDIR}/${PN}-salmon-v${PV}" - -PATCHES=( "${FILESDIR}/${PN}-do-not-fetch.patch" ) - -src_prepare() { - mkdir -p external/{setcover,seqlib} - mv "../setcover-${SC_COMMIT}"/* external/setcover || die - mv "../SeqLib-${SL_COMMIT}"/* external/seqlib || die - mv "../htslib-${HL_COMMIT}"/* external/seqlib/htslib || die - cmake_src_prepare -} |