sci-biology/*: remove revdeps of io_lib

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

26 files changed, 0 insertions, 934 deletions

diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest
deleted file mode 100644
index 761665281..000000000
--- a/sci-biology/caftools/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST caftools-2.0.2.tar.gz 2645554 BLAKE2B a48d8fb71500b5dc07da37467a9dc8d5972dfd7f63ae19cf7ca016774c3a23c4a9cd0f4caa1bde8efe5ef74c2576b8143f8b7375f9bf34414edcb14ed34a17d2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d
-DIST caftools-2.0.tar.gz 2644892 BLAKE2B 76aa90bf18d7543eb8f39de3e3be5fbca9a549e47341b032dd569394865ae02e269ea54a607acca2d88d404d271f78e1b97399bc8bdc1a107937163c89642323 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
deleted file mode 100644
index 7d58f3375..000000000
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/"
-SRC_URI="
-	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
-	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz"
-
-LICENSE="GRL"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	sci-libs/io_lib
-	dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/Makefile.in-"${PV}".patch
-)
-
-src_prepare(){
-	default
-	mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die
-}
-
-src_configure(){
-	default
-	sed \
-		-e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \
-		-i Makefile src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
-	default
-	doman man/*.[1-5] || die
-	elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/"
-	elog "for some reason caf_find_misassemblies is gone from 2.0.2 version"
-}
diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch
deleted file mode 100644
index 1e5160487..000000000
--- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- src/Makefile.in.ori	2010-12-05 22:59:40.000000000 +0100
-+++ src/Makefile.in	2010-12-05 23:01:19.000000000 +0100
-@@ -32,8 +32,6 @@
- includedir = @includedir@
- oldincludedir = /usr/include
- 
--DESTDIR =
--
- pkgdatadir = $(datadir)/@PACKAGE@
- pkglibdir = $(libdir)/@PACKAGE@
- pkgincludedir = $(includedir)/@PACKAGE@
-@@ -323,18 +321,18 @@
- 
- install-binPROGRAMS: $(bin_PROGRAMS)
- 	@$(NORMAL_INSTALL)
--	$(mkinstalldirs) $(DESTDIR)$(bindir)
-+	$(mkinstalldirs) $(bindir)
- 	@list='$(bin_PROGRAMS)'; for p in $$list; do \
- 	  if test -f $$p; then \
--	    echo "  $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
--	     $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+	    echo "  $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
-+	     $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- 	  else :; fi; \
- 	done
- 
- uninstall-binPROGRAMS:
- 	@$(NORMAL_UNINSTALL)
- 	list='$(bin_PROGRAMS)'; for p in $$list; do \
--	  rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
-+	  rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
- 	done
- 
- .c.o:
-@@ -579,7 +577,7 @@
- 	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
- installdirs: installdirs-recursive
- installdirs-am:
--	$(mkinstalldirs)  $(DESTDIR)$(bindir)
-+	$(mkinstalldirs)  $(bindir)
- 
- 
- mostlyclean-generic:
diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch
deleted file mode 100644
index 4ddd9f628..000000000
--- a/sci-biology/caftools/files/Makefile.in.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- src/Makefile.in.ori	2010-12-05 22:08:50.000000000 +0100
-+++ src/Makefile.in	2010-12-05 22:10:07.000000000 +0100
-@@ -18,7 +18,7 @@
- srcdir = @srcdir@
- top_srcdir = @top_srcdir@
- VPATH = @srcdir@
--prefix = @prefix@
-+prefix = $(DESTDIR)/@prefix@
- exec_prefix = @exec_prefix@
- 
- bindir = @bindir@
-@@ -394,14 +394,14 @@
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
- install-binPROGRAMS: $(bin_PROGRAMS)
- 	@$(NORMAL_INSTALL)
--	$(mkinstalldirs) $(DESTDIR)$(bindir)
-+	$(mkinstalldirs) $(bindir)
- 	@list='$(bin_PROGRAMS)'; for p in $$list; do \
- 	  p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
- 	  if test -f $$p \
- 	  ; then \
- 	    f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
--	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \
--	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \
-+	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \
-+	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \
- 	  else :; fi; \
- 	done
- 
-@@ -409,8 +409,8 @@
- 	@$(NORMAL_UNINSTALL)
- 	@list='$(bin_PROGRAMS)'; for p in $$list; do \
- 	  f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
--	  echo " rm -f $(DESTDIR)$(bindir)/$$f"; \
--	  rm -f $(DESTDIR)$(bindir)/$$f; \
-+	  echo " rm -f $(bindir)/$$f"; \
-+	  rm -f $(bindir)/$$f; \
- 	done
- 
- clean-binPROGRAMS:
-@@ -663,7 +663,7 @@
- all-am: Makefile $(PROGRAMS) config.h
- installdirs: installdirs-recursive
- installdirs-am:
--	$(mkinstalldirs) $(DESTDIR)$(bindir)
-+	$(mkinstalldirs) $(bindir)
- 
- install: install-recursive
- install-exec: install-exec-recursive
diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml
deleted file mode 100644
index 224641279..000000000
--- a/sci-biology/caftools/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-CAF is a text format for describing sequence assemblies. It is acedb-compliant
-and is an extension of the ace-file format used earlier, but with support for 
-base quality measures and a more extensive description of the Sequence data.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/roche454ace2caf/Manifest b/sci-biology/roche454ace2caf/Manifest
deleted file mode 100644
index 6711cecd3..000000000
--- a/sci-biology/roche454ace2caf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST roche454ace2gap-2010-12-08.tgz 261317 BLAKE2B e00ba3b1d19c9856447c74d3943854e2c6556c14ef19a1abe73a6e0375b8e889c57b4c00beda2f9f9adf6cb76f6f89a12bfe9c9782b5668c0f883e914fa68204 SHA512 ce477ab88c45e947764d0dcb667f76de195db8f1ebc53ca6892f74017a79e231f77c458564a9ac682679bb6b486493ee6692157628401351de5a732894e5a732
diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-biology/roche454ace2caf/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/roche454ace2caf/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
deleted file mode 100644
index a3c4eee39..000000000
--- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="ace to gap4 converter"
-HOMEPAGE="https://genome.imb-jena.de/software/roche454ace2caf/"
-SRC_URI="https://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz"
-
-LICENSE="FLI-Jena"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	sci-biology/align_to_scf
-	sci-biology/sff_dump
-	sci-biology/caftools
-	sci-biology/staden
-	dev-lang/perl
-	app-shells/ksh"
-
-S="${WORKDIR}/roche2gap"
-
-src_install(){
-	dobin bin/*.pl bin/roche454ace2gap
-	einstalldocs
-}
diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
deleted file mode 100644
index 37410d297..000000000
--- a/sci-biology/salmon/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
-DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
-DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
-DIST libgff-salmon-1.6.0.tar.gz 102152 BLAKE2B 56bccaadf82fe51db4f6297177b3c49d7ab4fe858719e3a689834ef10b63dd0ffabba2424771865efab1bd226dccb3a104307ef406e3861e762426cfcc5de543 SHA512 c5e84fad659502134e90c45a0075e79fe1dcf84d08ec4820c337b898fae24c8fe3985cb5fb3e653a13d1756179730ff0cae53bb2c78fe37038f7bd9c7eae85e2
-DIST pufferfish-salmon-1.6.0.tar.gz 3119250 BLAKE2B f3db6506d003418fcaeeb78c114acc0dcd89d745d2433dcbf87dc8ff8dbec15299a799b469f6a07fd07f85afd925c85643c3791819413db3fc14de5686ae112f SHA512 82c1137a14ef7773101b35070b6a943213443d98e218118e6a5c2df1cab860ed9543bcac3b7408e0b7eeb74fe1997d521b4883515a964d03813bcea8b2bfaa8d
-DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
-DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
-DIST salmon-1.6.0.tar.gz 7145603 BLAKE2B 5ffa9bd8cdd76232caaa736ffb959922b47f934217bd706417431f92c406f407529b5df67b13506df4365ce56676b70cf470466cdf616d097c96a8cd312d34d5 SHA512 580292b48165ba6db48db44d3e57e5020410f29a48b4015445c4c354e81989ff872e8874e2a7aab128362f178819330fbdc2a11089189bfbc8cd3058fc0eb4d6
-DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
-DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
deleted file mode 100644
index ac561d793..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt	2018-06-25 10:51:47.179712781 +0200
-+++ salmon-0.10.2/CMakeLists.txt	2018-06-25 10:52:47.951289159 +0200
-@@ -213,15 +213,6 @@
-     set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
- 
--##
--# We want static, multithreaded boost libraries
--##
--if(CONDA_BUILD)
--  set (Boost_USE_STATIC_LIBS OFF)
--else ()
--  set (Boost_USE_STATIC_LIBS ON)
--endif(CONDA_BUILD)
--
- set (Boost_USE_MULTITHREADED ON)
- #set (Boost_USE_STATIC_RUNTIME OFF)
- 
diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
deleted file mode 100644
index 81edf96f5..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake	2018-06-26 10:39:51.061971241 +0200
-+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake	2018-06-26 10:40:22.372822258 +0200
-@@ -5,7 +5,7 @@
-                 )
- 
- if (SALMON_QUASI_INDEX_RESULT)
--    message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}")
-+    message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}")
- endif()
- 
- set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant)
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
deleted file mode 100644
index eb606c00c..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt	2018-06-25 13:35:45.723519730 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt	2018-06-25 13:44:01.326139539 +0200
-@@ -296,6 +296,8 @@
-     )
- ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
- 
-+include(GNUInstallDirs)
-+
- set(INSTALL_LIB_DIR lib )
- set(INSTALL_BIN_DIR bin )
- set(INSTALL_INCLUDE_DIR include )
-@@ -311,8 +313,8 @@
- 
- install(TARGETS salmon salmon_core
-                 RUNTIME DESTINATION bin
--                LIBRARY DESTINATION lib
--                ARCHIVE DESTINATION lib
-+                LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
-+                ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
-         )
- 
- add_custom_command(TARGET unitTests POST_BUILD
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
deleted file mode 100644
index 0a95757a8..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- salmon-0.10.2/src/CMakeLists.txt.ori	2018-06-26 10:34:29.293225671 +0200
-+++ salmon-0.10.2/src/CMakeLists.txt	2018-06-26 10:35:24.674730920 +0200
-@@ -335,6 +335,6 @@
- )
- 
- include(InstallRequiredSystemLibraries)
--add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
-+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
- add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake )
- add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake )
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
deleted file mode 100644
index 8eddc6e3a..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- salmon-9999/scripts/fetchRapMap.sh	2018-06-25 11:11:07.019798309 +0200
-+++ salmon-9999/scripts/fetchRapMap.sh	2018-06-25 11:12:25.131824486 +0200
-@@ -29,7 +29,8 @@
- EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688
- 
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
-+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip
- 
- hashcheck=""
- if exists sha256sum; then
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
deleted file mode 100644
index 438763960..000000000
--- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch
+++ /dev/null
@@ -1,200 +0,0 @@
---- salmon-0.10.2/CMakeLists.txt	2018-06-25 13:12:49.275828719 +0200
-+++ salmon-0.10.2/CMakeLists.txt	2018-06-25 13:12:38.945565690 +0200
-@@ -235,31 +235,7 @@
- 
- find_package (LibLZMA)
- if (NOT LIBLZMA_FOUND)
--    message ("Will attempt to fetch and build liblzma")
--    message ("=======================================")
--ExternalProject_Add(liblzma
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    ##
--    DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz &&
--                     ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz &&
--                     tar -xzvf xz-5.2.2.tar.gz
--    #URL http://tukaani.org/xz/xz-5.2.2.tar.gz
--    #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08
--    ##
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
--    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    BUILD_IN_SOURCE TRUE
--    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS}
--    BUILD_COMMAND make ${QUIET_MAKE}
--    INSTALL_COMMAND make ${QUIET_MAKE} install
--)
--
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBLZMA TRUE)
-+    message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed")
- else()
-     message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
-     message("===========================================")
-@@ -267,28 +243,7 @@
- 
- find_package (BZip2)
- if (NOT BZIP2_FOUND)
--    message ("Will attempt to fetch and build libbz2")
--    message ("=======================================")
--ExternalProject_Add(libbz2
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz &&
--                     ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz &&
--                     tar -xzvf  bzip2-1.0.6.tar.gz
--    #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
--    #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
--    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    BUILD_IN_SOURCE TRUE
--    CONFIGURE_COMMAND ""
--    BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
--    INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
--)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBBZ2 TRUE)
-+    message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed")
- else()
-     message("Found libbz2 library: ${BZIP2_LIBRARIES}")
-     message("===========================================")
-@@ -333,61 +288,15 @@
- # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
- # option, go and grab it for them.
- ##
--if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
-+if (NOT Boost_FOUND)
- 	message(FATAL_ERROR
-         "Salmon cannot be compiled without Boost.\n"
-         "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
-         "This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
-         "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
-     )
--elseif(FETCH_BOOST)
--    ## Let the rest of the build process know we're going to be fetching boost
--    set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
--                          --with-filesystem --with-graph --with-graph_parallel --with-math
--                          --with-program_options --with-system --with-thread
--                          --with-timer)
--    set (BOOST_WILL_RECONFIGURE TRUE)
--    set (FETCH_BOOST FALSE)
--    message("Build system will fetch and build Boost")
--    message("==================================================================")
--    ExternalProject_Add(libboost
--        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--        DOWNLOAD_COMMAND curl -k -L  http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz &&
--                         ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz &&
--                         tar xzf boost_1_66_0.tar.gz
--        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0
--        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--        #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
--	CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
--	BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install
--        BUILD_IN_SOURCE 1
--        INSTALL_COMMAND ""
--    )
--
--    ##
--    # After we've installed boost,
--    ##
--    SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
--    ExternalProject_Add_Step(libboost reconfigure
--        COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
--        DEPENDEES install
--    )
--    set (FETCHED_BOOST TRUE)
- endif()
- 
--##
--# If we're fetching boost and we need to have dummy paths for these variables
--# so that CMake won't complain
--##
--if (BOOST_WILL_RECONFIGURE)
--    message("Setting Temporary Boost paths")
--    set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
--    set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
--    set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
--    set(Boost_FOUND TRUE)
--endif()
--
--
- message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
- message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
- message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
-@@ -422,9 +331,9 @@
- include(ExternalProject)
- ExternalProject_Add(libcereal
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz &&		 
--                     ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4  cereal-v1.2.2.tar.gz &&
--                     tar -xzvf cereal-v1.2.2.tar.gz
-+    DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . &&		 
-+                     ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4  cereal-1.2.2.tar.gz &&
-+                     tar -xzvf cereal-1.2.2.tar.gz
- 
-     ##
-     #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz
-@@ -455,12 +364,12 @@
- ExternalProject_Add(libbwa
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-     #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz
--    #DOWNLOAD_NAME bwa-master.tar.gz
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz &&
--                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz &&
--                    mkdir -p bwa-master &&
--                    tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
-+    #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz
-+    DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . &&
-+                    ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz &&
-+                    mkdir -p bwa-0.7.12.5 &&
-+                    tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5
-+    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5
-     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-     CONFIGURE_COMMAND ""
-     BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
-@@ -562,9 +471,9 @@
- message("==================================================================")
- ExternalProject_Add(libgff
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
--                     ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697  libgff.tgz &&
--                     tar -xzvf libgff.tgz 
-+    DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . &&
-+                     ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz &&
-+                     tar -xzvf libgff-1.1.tgz
-     ##
-     #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-     #DOWNLOAD_NAME libff.tgz
-@@ -600,10 +509,10 @@
- message("==================================================================")
- ExternalProject_Add(libstadenio
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
--                     ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz &&
-+    DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . &&
-+                     ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz &&
-                      mkdir -p staden-io_lib-1.14.8 &&
--                     tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-+                     tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-                      rm -fr staden-io_lib &&
-                      mv -f staden-io_lib-1.14.8 staden-io_lib
-     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
-@@ -620,9 +529,9 @@
- message("==================================================================")
- ExternalProject_Add(libspdlog
-     DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz &&
--                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz &&
--                     tar -xzf spdlog-v0.16.1.tar.gz 
-+    DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . &&
-+                     ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz &&
-+                     tar -xzf spdlog-0.16.1.tar.gz 
-     ##
-     #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz
-     #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz
diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
deleted file mode 100644
index 76ef25547..000000000
--- a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be02ab..48ffda2 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -428,9 +428,9 @@ endif()
- ##
- # Set the latest version and look for what we need
- ##
--set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0")
-+set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0")
- if (NOT BOOST_RECONFIGURE)
--find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
-+find_package(Boost 1.59.0 COMPONENTS ALL)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message("Boost_FOUND = ${Boost_FOUND}")
-@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
- endif()
- 
- ## Try and find TBB first
--find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
-+find_package(TBB)
- 
- ## NOTE: we actually require at least 2019 U4 or greater
- ## since we are using tbb::global_control.  However, they 
-@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
- ## source.  Check before release if we can bump to the 2020
- ## version (requires having tbb 2020 for OSX).
- if (${TBB_FOUND})
--  if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
-   message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
-   set(TBB_TARGET_EXISTED TRUE)
--  else()
--    set(TBB_TARGET_EXISTED FALSE)
--  endif()
- else()
-   set(TBB_TARGET_EXISTED FALSE)
- endif()
-@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
-   message("Build system will compile libgff")
-   message("==================================================================")
-   externalproject_add(libgff
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
--      ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
--      tar -xzvf libgff.tgz
-     ##
-     #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-     #DOWNLOAD_NAME libff.tgz
-diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
-index c8b3eb5..b4c23da 100644
---- a/cmake/Modules/FindTBB.cmake
-+++ b/cmake/Modules/FindTBB.cmake
-@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
-   ##################################
- 
-   if(TBB_INCLUDE_DIRS)
--    file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
-     string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
-         TBB_VERSION_MAJOR "${_tbb_version_file}")
-     string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
-diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
-index d32e131..1b5cbf2 100755
---- a/scripts/fetchPufferfish.sh
-+++ b/scripts/fetchPufferfish.sh
-@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
- EXTERNAL_DIR=${CURR_DIR}/../external
- INSTALL_DIR=${CURR_DIR}/../external/install
- 
--if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
--    rm -fr ${EXTERNAL_DIR}/pufferfish
--fi
--
--if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
--    rm -fr ${INSTALL_DIR}/include/pufferfish
--fi
--
--if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
--    rm -fr ${INSTALL_DIR}/src/pufferfish
--fi
--
- SVER=salmon-v1.6.0
- #SVER=develop
- #SVER=sketch-mode
-@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
- EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
- 
- mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
--
--hashcheck=""
--if exists sha256sum; then
--	hashcheck="sha256sum"
--elif exists shasum; then
--	hashcheck="shasum -a256"
--else
--	unset hashcheck
--fi
--
--if [ -z "${hashcheck-}" ]; then
--    echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
--else
--    if [[ $SVER != develop ]]; then
--        echo "${EXPECTED_SHA256}  ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
--    else
--        echo "not testing sha since pulling from develop"
--    fi
--fi
--
--
--rm -fr ${EXTERNAL_DIR}/pufferfish
--unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
- 
- mkdir -p ${INSTALL_DIR}/include/pufferfish
- 
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
deleted file mode 100644
index 1907254d6..000000000
--- a/sci-biology/salmon/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>mschu.dev@gmail.com</email>
-		<name>Michael Schubert</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">COMBINE-lab/salmon</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
deleted file mode 100644
index c3ef9e50a..000000000
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
-	https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
-	https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
-	https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
-	https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
-	https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
-		"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
-		"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
-		"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
-		"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
-		"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-RDEPEND="${DEPEND}"
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-#    actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-#    https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
-#
-DEPEND="
-	sys-libs/zlib
-	app-arch/bzip2
-	app-arch/xz-utils
-	dev-libs/boost:0=
-	dev-libs/libdivsufsort
-	sci-biology/bwa
-	>=dev-libs/jemalloc-5.0.1
-	>=dev-cpp/tbb-2018.20180312
-"
-RDEPEND="${DEPEND}"
-BDEPEND="
-	net-misc/curl
-	app-arch/unzip
-"
-
-src_prepare() {
-	# use system libs
-	sed -i \
-		-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \
-		-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \
-		-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \
-		-e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \
-		src/CMakeLists.txt || die
-
-	cmake_src_prepare
-}
diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild
deleted file mode 100644
index 6c19ff58f..000000000
--- a/sci-biology/salmon/salmon-1.6.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="
-	https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
-	https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
-"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	dev-libs/boost:=
-	sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
-	app-arch/bzip2
-	app-arch/xz-utils
-	>=dev-libs/jemalloc-5.0.1
-	>=dev-cpp/tbb-2018.20180312
-	dev-libs/cereal
-	sci-libs/io_lib[static-libs]
-"
-
-BDEPEND="
-	app-arch/unzip
-	net-misc/curl
-"
-
-PATCHES=(
-	"${FILESDIR}/${P}-find-boost.patch"
-)
-
-src_unpack() {
-	default
-	mkdir -p "${S}/external/install/lib" || die
-	mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
-	mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
-	ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
-	ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
-	ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
-}
-
-src_prepare() {
-	cmake_src_prepare
-	sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
-		-i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
-		-i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DFETCH_BOOST=FALSE
-		-DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
-		-DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
-		-DBoost_ALL_FOUND=TRUE
-		-Dboost_headers_FOUND=TRUE
-		-DBoost_FOUND=TRUE
-	)
-	cmake_src_configure
-}
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
deleted file mode 100644
index 13f7d3536..000000000
--- a/sci-biology/staden/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST staden-2.0.0_beta11-src.tar.gz 4754651 BLAKE2B d55dcff2192a5f6c505d141960f624ad30afb358e481c438d285a267bb116f8e26e1b7d6562c222b4c7392729bacd14524ee9275ada5201b7d8bcefbd244112f SHA512 6f85cc3aa3b909431333a4998566b267f1d344b3160603604306caf41504cc36c05980790bf5a8f2b4a53f7aea2a369ffafbce163b41c3ea94605f7fee07a26a
diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
- 
- getABIdate: $(OBJSD)
--	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
- 
- getABIcomment: $(OBJSC)
- 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
- 
- alfsplit: $(ALFOBJ)
--	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
- 
- RSOBJ = $(ALFBIN)/2rs.o
- 
diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">staden</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild
deleted file mode 100644
index a0f91720b..000000000
--- a/sci-biology/staden/staden-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic fortran-2
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-
-DEPEND="
-	app-arch/xz-utils
-	dev-lang/tk:0=
-	dev-tcltk/tklib
-	media-libs/libpng:0
-	sci-biology/samtools:0
-	>=sci-libs/io_lib-1.13.8
-	sys-libs/zlib"
-RDEPEND="${DEPEND}
-	>=dev-tcltk/iwidgets-4.0
-	tcl? ( >=dev-tcltk/itcl-3.2 )
-	tk? ( >=dev-tcltk/itk-3.2 )
-	net-misc/curl
-	doc? ( sci-biology/staden_doc )"
-
-S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src
-
-PATCHES=(
-	"${FILESDIR}/${P}-ldflags.patch"
-)
-
-src_prepare() {
-	default
-	sed \
-		-e 's:svnversion:false:' \
-		-i configure.in || die
-}
-
-src_configure(){
-	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	econf \
-		$(use_enable X x) \
-		$(use_enable amd64 64bit) \
-		--with-tklib="/usr/$(get_libdir)/tklib"
-}
-
-src_install() {
-	default
-	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
-	# subsequently, apps linked against /usr/lib/staden can be run because
-	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
-	# somehow for gap2caf, for example
-	cat >> "${T}"/99staden <<- EOF
-	STADENROOT="${EPREFIX}"/usr/share/staden
-	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
-	EOF
-	doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
-	einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest
deleted file mode 100644
index 108aad2fe..000000000
--- a/sci-biology/staden_doc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST staden_doc-2.0.0b11-src.tar.gz 3184526 BLAKE2B cf67f702efd0743899b0f955434b815bdb695d28641069a4da981e5fe5de9091980b997e55d10897ff21fca1928f1afb787aa9a89d66ab658b14f8db9b35d110 SHA512 ca8aad2ab3ec660dbd8631bb65df95b10fa64e20d5d509925a03e277896ed8a2eebef89f6b170fe2acd0dd10e0075585620dd162b7b5c9153b248ee6dedd6ef1
diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml
deleted file mode 100644
index 1ed1820a4..000000000
--- a/sci-biology/staden_doc/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">staden</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
deleted file mode 100644
index 5a70701b0..000000000
--- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Documentation files for the staden package"
-HOMEPAGE="https://sourceforge.net/projects/staden"
-SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
-	dev-lang/perl
-	app-text/texlive
-	app-text/texi2html"
-BDEPEND="app-editors/emacs"
-RDEPEND="${DEPEND} ${BDEPEND}"
-
-S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src
-
-# do not use texi2html-5 because it fails with:
-# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo
-# Unknown option: index_char
-# src_prepare(){
-# 	default
-# 	# avoid running bundled texi2html code
-# 	sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die
-# }
-
-src_compile(){
-	cd manual || die
-	emake -j1 spotless || die
-	cd .. || die
-	emake -j1 unix PAPER=A4
-}
-
-src_install(){
-	emake -j1 install prefix="${D}"/usr
-	dodoc gkb547_gml.pdf
-}