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-rw-r--r--sci-biology/Fastaq/metadata.xml5
-rw-r--r--sci-biology/MolBioLib/metadata.xml5
-rw-r--r--sci-biology/Rcorrector/metadata.xml7
-rw-r--r--sci-biology/Scaffolder-evaluation/metadata.xml5
-rw-r--r--sci-biology/SnpEff/metadata.xml5
-rw-r--r--sci-biology/VarScan-bin/metadata.xml3
-rw-r--r--sci-biology/VarScan/metadata.xml3
-rw-r--r--sci-biology/assembly-stats/metadata.xml5
-rw-r--r--sci-biology/bam-readcount/metadata.xml5
-rw-r--r--sci-biology/bedops/Manifest1
-rw-r--r--sci-biology/bedops/bedops-2.4.26.ebuild25
-rw-r--r--sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch138
-rw-r--r--sci-biology/bedops/metadata.xml12
-rw-r--r--sci-biology/bfast/metadata.xml5
-rw-r--r--sci-biology/bio-cd-hit-report/metadata.xml5
-rw-r--r--sci-biology/cd-hit/metadata.xml5
-rw-r--r--sci-biology/conrad/metadata.xml5
-rw-r--r--sci-biology/cramtools/metadata.xml5
-rw-r--r--sci-biology/cross_genome/metadata.xml5
-rw-r--r--sci-biology/cutadapt/metadata.xml3
-rw-r--r--sci-biology/deeptools/metadata.xml5
-rw-r--r--sci-biology/ensembl-tools/metadata.xml5
-rw-r--r--sci-biology/fgap-bin/metadata.xml5
-rw-r--r--sci-biology/fgap/metadata.xml5
-rw-r--r--sci-biology/flexbar/metadata.xml3
-rw-r--r--sci-biology/gemini/metadata.xml5
-rw-r--r--sci-biology/grabix/metadata.xml5
-rw-r--r--sci-biology/grass/metadata.xml7
-rw-r--r--sci-biology/hisat2/metadata.xml5
-rw-r--r--sci-biology/hts-python/metadata.xml5
-rw-r--r--sci-biology/jannovar-bin/metadata.xml7
-rw-r--r--sci-biology/jannovar/metadata.xml5
-rw-r--r--sci-biology/jtreeview-bin/metadata.xml5
-rw-r--r--sci-biology/jtreeview/metadata.xml3
-rw-r--r--sci-biology/karect/metadata.xml5
-rw-r--r--sci-biology/kat/metadata.xml5
-rw-r--r--sci-biology/libBigWig/metadata.xml5
-rw-r--r--sci-biology/lumpy-sv/metadata.xml5
-rw-r--r--sci-biology/megahit/metadata.xml5
-rw-r--r--sci-biology/mothur/metadata.xml5
-rw-r--r--sci-biology/ncbi-blast+/Manifest2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild (renamed from sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild)8
-rw-r--r--sci-biology/nilearn/metadata.xml3
-rw-r--r--sci-biology/nwalign/metadata.xml7
-rw-r--r--sci-biology/nxtrim/metadata.xml5
-rw-r--r--sci-biology/oncotator/metadata.xml5
-rw-r--r--sci-biology/perga/metadata.xml5
-rw-r--r--sci-biology/phusion2/metadata.xml7
-rw-r--r--sci-biology/picard/metadata.xml3
-rw-r--r--sci-biology/prinseq-lite/metadata.xml5
-rw-r--r--sci-biology/psychopy/metadata.xml3
-rw-r--r--sci-biology/pybrain/metadata.xml5
-rw-r--r--sci-biology/pysamstats/metadata.xml6
-rw-r--r--sci-biology/ruffus/metadata.xml7
-rw-r--r--sci-biology/sambamba/metadata.xml5
-rw-r--r--sci-biology/scbi_blast/metadata.xml3
-rw-r--r--sci-biology/scbi_fasta/metadata.xml3
-rw-r--r--sci-biology/scbi_fastq/metadata.xml5
-rw-r--r--sci-biology/scbi_mapreduce/metadata.xml3
-rw-r--r--sci-biology/scbi_plot/metadata.xml3
-rw-r--r--sci-biology/scbi_zcat/metadata.xml5
-rw-r--r--sci-biology/smalt/metadata.xml7
-rw-r--r--sci-biology/snpomatic/metadata.xml5
-rw-r--r--sci-biology/somatic-sniper/metadata.xml5
-rw-r--r--sci-biology/staden_doc/metadata.xml5
-rw-r--r--sci-biology/stringtie/metadata.xml5
-rw-r--r--sci-biology/vcflib/metadata.xml5
-rw-r--r--sci-biology/vcftools/metadata.xml3
-rw-r--r--sci-biology/verifyBamID/metadata.xml5
-rw-r--r--sci-biology/vt/metadata.xml5
-rw-r--r--sci-biology/yaha/metadata.xml5
71 files changed, 424 insertions, 76 deletions
diff --git a/sci-biology/Fastaq/metadata.xml b/sci-biology/Fastaq/metadata.xml
index f68a1b6fa..04b6bd54b 100644
--- a/sci-biology/Fastaq/metadata.xml
+++ b/sci-biology/Fastaq/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">sanger-pathogens/Fastaq</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml
index f68a1b6fa..cfa9e50ee 100644
--- a/sci-biology/MolBioLib/metadata.xml
+++ b/sci-biology/MolBioLib/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">molbiolib</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/Rcorrector/metadata.xml b/sci-biology/Rcorrector/metadata.xml
index 1699e58b2..7cca6fb36 100644
--- a/sci-biology/Rcorrector/metadata.xml
+++ b/sci-biology/Rcorrector/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">mourisl/Rcorrector</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/Scaffolder-evaluation/metadata.xml b/sci-biology/Scaffolder-evaluation/metadata.xml
index f68a1b6fa..ede9259b5 100644
--- a/sci-biology/Scaffolder-evaluation/metadata.xml
+++ b/sci-biology/Scaffolder-evaluation/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">martinghunt/Scaffolder-evaluation</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml
index f68a1b6fa..c7accda31 100644
--- a/sci-biology/SnpEff/metadata.xml
+++ b/sci-biology/SnpEff/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">snpeff</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/VarScan-bin/metadata.xml b/sci-biology/VarScan-bin/metadata.xml
index fae01f1fa..e27dba2e9 100644
--- a/sci-biology/VarScan-bin/metadata.xml
+++ b/sci-biology/VarScan-bin/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">varscan</remote-id>
+ <remote-id type="github">dkoboldt/varscan</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/VarScan/metadata.xml b/sci-biology/VarScan/metadata.xml
index fae01f1fa..e27dba2e9 100644
--- a/sci-biology/VarScan/metadata.xml
+++ b/sci-biology/VarScan/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">varscan</remote-id>
+ <remote-id type="github">dkoboldt/varscan</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/assembly-stats/metadata.xml b/sci-biology/assembly-stats/metadata.xml
index f68a1b6fa..e528fb05f 100644
--- a/sci-biology/assembly-stats/metadata.xml
+++ b/sci-biology/assembly-stats/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">martinghunt/assembly-stats</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bam-readcount/metadata.xml b/sci-biology/bam-readcount/metadata.xml
index f68a1b6fa..2f50f6cb0 100644
--- a/sci-biology/bam-readcount/metadata.xml
+++ b/sci-biology/bam-readcount/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">genome/bam-readcount</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bedops/Manifest b/sci-biology/bedops/Manifest
new file mode 100644
index 000000000..54a156cc2
--- /dev/null
+++ b/sci-biology/bedops/Manifest
@@ -0,0 +1 @@
+DIST bedops-2.4.26.tar.gz 27057360 SHA256 9b8ff43beec7b6e327179477b800a9c7ce98a010bbf59ba41fc2d7da9869586d SHA512 6c43ff4f42168da8e181e5d50e8d41a1c0a8c24bde3ca6ab81f9b2324d47b4f7d265e3031adf39ea7ad0e65773462d13ed59580774f5a0906b205b27648a8eaa WHIRLPOOL ad25d562dee5a51f10ee66d5a74984071b6aaddb1cde139b8fa2b420a2b6b10860c389eaf59f74c5fabc09851629f366747e7330432c0aa9c9d174606a3ffbfb
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
new file mode 100644
index 000000000..d281fbede
--- /dev/null
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs eutils
+
+DESCRIPTION="Manipulate BED file (alternative to bedtools)"
+HOMEPAGE="http://bedops.readthedocs.io
+ https://github.com/bedops/bedops"
+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ default
+ local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
+ epatch ${PATCHES[@]}
+}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
new file mode 100644
index 000000000..16ac4e2b0
--- /dev/null
+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
@@ -0,0 +1,138 @@
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200
+@@ -24,7 +24,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+@@ -64,4 +64,4 @@
+ rm -rf $(OBJDIR)
+ rm -f $(BINDIR)/$(PROG)
+ rm -f $(BINDIR)/*.$(PROG)
+- rm -rf $(BINDIR)
+\ No newline at end of file
++ rm -rf $(BINDIR)
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200
+@@ -1,7 +1,7 @@
+ MIN_OSX_VERSION = 10.7
+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS = -O3
++CFLAGS = ${CXXFLAGS:--O3}
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200
+@@ -1,6 +1,6 @@
+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS = -O3
++CFLAGS = ${CXXFLAGS:--O3}
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200
+@@ -27,7 +27,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200
+@@ -25,7 +25,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200
+@@ -7,7 +7,7 @@
+ PROG = sort-bed
+ DIST_DIR = ../bin
+ OBJ_DIR = objects_${ARCH}
+-OPTIMIZE = -O3 -std=c++11 -stdlib=libc++
++OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
+ WARNINGS = -Wall
+ MAIN = ../../../..
+ HEAD = ${MAIN}/interfaces/general-headers
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200
+@@ -29,7 +29,7 @@
+ BINDIR = ../bin
+ OBJDIR = objects
+ WARNINGS = -Wall -Wextra -pedantic
+-BLDFLAGS = ${WARNINGS} -O3 -std=c++11
++BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/bedops/metadata.xml
@@ -0,0 +1,12 @@
+<?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/bfast/metadata.xml b/sci-biology/bfast/metadata.xml
index f68a1b6fa..45f337087 100644
--- a/sci-biology/bfast/metadata.xml
+++ b/sci-biology/bfast/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">bfast</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/bio-cd-hit-report/metadata.xml b/sci-biology/bio-cd-hit-report/metadata.xml
index f68a1b6fa..ed211409a 100644
--- a/sci-biology/bio-cd-hit-report/metadata.xml
+++ b/sci-biology/bio-cd-hit-report/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="rubygems">bio-cd-hit-report</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
index 2880d6633..1f3b07521 100644
--- a/sci-biology/cd-hit/metadata.xml
+++ b/sci-biology/cd-hit/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
@@ -19,8 +19,9 @@ datasets and identifies the sequences in db2 that are similar to db1 above
a threshold. CD-HIT-454 is a program to identify natural and artificial
duplicates from pyrosequencing reads. The usage of other programs and
scripts can be found in CD-HIT user's guide.
-</longdescription>
+ </longdescription>
<upstream>
<remote-id type="google-code">cdhit</remote-id>
+ <remote-id type="github">weizhongli/cdhit</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
index f68a1b6fa..8d38b0b1a 100644
--- a/sci-biology/conrad/metadata.xml
+++ b/sci-biology/conrad/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">conradcrf</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml
index f68a1b6fa..0a1821f4a 100644
--- a/sci-biology/cramtools/metadata.xml
+++ b/sci-biology/cramtools/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">enasequence/cramtools</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/cross_genome/metadata.xml b/sci-biology/cross_genome/metadata.xml
index f68a1b6fa..18786886b 100644
--- a/sci-biology/cross_genome/metadata.xml
+++ b/sci-biology/cross_genome/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">phusion2</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml
index dde730ca4..d432ff9a4 100644
--- a/sci-biology/cutadapt/metadata.xml
+++ b/sci-biology/cutadapt/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="pypi">cutadapt</remote-id>
+ <remote-id type="github">marcelm/cutadapt</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/deeptools/metadata.xml b/sci-biology/deeptools/metadata.xml
index f68a1b6fa..ae7de7d62 100644
--- a/sci-biology/deeptools/metadata.xml
+++ b/sci-biology/deeptools/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">fidelram/deepTools</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml
index f68a1b6fa..2457da65b 100644
--- a/sci-biology/ensembl-tools/metadata.xml
+++ b/sci-biology/ensembl-tools/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">Ensembl/ensembl-tools</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/fgap-bin/metadata.xml b/sci-biology/fgap-bin/metadata.xml
index f68a1b6fa..59e8a4413 100644
--- a/sci-biology/fgap-bin/metadata.xml
+++ b/sci-biology/fgap-bin/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">fgap</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/fgap/metadata.xml b/sci-biology/fgap/metadata.xml
index f68a1b6fa..59e8a4413 100644
--- a/sci-biology/fgap/metadata.xml
+++ b/sci-biology/fgap/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">fgap</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/flexbar/metadata.xml b/sci-biology/flexbar/metadata.xml
index ce8e58909..6bf81a0d4 100644
--- a/sci-biology/flexbar/metadata.xml
+++ b/sci-biology/flexbar/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">flexbar</remote-id>
+ <remote-id type="github">seqan/flexbar</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml
index f68a1b6fa..745bce5e5 100644
--- a/sci-biology/gemini/metadata.xml
+++ b/sci-biology/gemini/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">arq5x/gemini</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/grabix/metadata.xml b/sci-biology/grabix/metadata.xml
index f68a1b6fa..5ad9ab32c 100644
--- a/sci-biology/grabix/metadata.xml
+++ b/sci-biology/grabix/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">arq5x/grabix</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml
index 1699e58b2..8563b702d 100644
--- a/sci-biology/grass/metadata.xml
+++ b/sci-biology/grass/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">AlexeyG/GRASS</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml
index f68a1b6fa..b28711aa3 100644
--- a/sci-biology/hisat2/metadata.xml
+++ b/sci-biology/hisat2/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">infphilo/hisat2</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/hts-python/metadata.xml b/sci-biology/hts-python/metadata.xml
index f68a1b6fa..39221baa1 100644
--- a/sci-biology/hts-python/metadata.xml
+++ b/sci-biology/hts-python/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">brentp/hts-python</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/jannovar-bin/metadata.xml b/sci-biology/jannovar-bin/metadata.xml
index 1699e58b2..faceb6e46 100644
--- a/sci-biology/jannovar-bin/metadata.xml
+++ b/sci-biology/jannovar-bin/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">charite/jannovar</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/jannovar/metadata.xml b/sci-biology/jannovar/metadata.xml
index f68a1b6fa..faceb6e46 100644
--- a/sci-biology/jannovar/metadata.xml
+++ b/sci-biology/jannovar/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">charite/jannovar</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/jtreeview-bin/metadata.xml b/sci-biology/jtreeview-bin/metadata.xml
index f68a1b6fa..40552f721 100644
--- a/sci-biology/jtreeview-bin/metadata.xml
+++ b/sci-biology/jtreeview-bin/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">jtreeview</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml
index 3b98c8e27..a7083bff9 100644
--- a/sci-biology/jtreeview/metadata.xml
+++ b/sci-biology/jtreeview/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">jtreeview</remote-id>
+ <remote-id type="bitbucket">TreeView3Dev/treeview3</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/karect/metadata.xml b/sci-biology/karect/metadata.xml
index f68a1b6fa..0ac12d618 100644
--- a/sci-biology/karect/metadata.xml
+++ b/sci-biology/karect/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">aminallam/karect</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml
index f68a1b6fa..5561548a6 100644
--- a/sci-biology/kat/metadata.xml
+++ b/sci-biology/kat/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">TGAC/KAT</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/libBigWig/metadata.xml b/sci-biology/libBigWig/metadata.xml
index f68a1b6fa..dafe9d1fd 100644
--- a/sci-biology/libBigWig/metadata.xml
+++ b/sci-biology/libBigWig/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">dpryan79/libBigWig</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/lumpy-sv/metadata.xml b/sci-biology/lumpy-sv/metadata.xml
index f68a1b6fa..27a0e1f28 100644
--- a/sci-biology/lumpy-sv/metadata.xml
+++ b/sci-biology/lumpy-sv/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">arq5x/lumpy-sv</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/megahit/metadata.xml b/sci-biology/megahit/metadata.xml
index f68a1b6fa..deaf720d8 100644
--- a/sci-biology/megahit/metadata.xml
+++ b/sci-biology/megahit/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">voutcn/megahit</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
index 959160fe4..9afdf8282 100644
--- a/sci-biology/mothur/metadata.xml
+++ b/sci-biology/mothur/metadata.xml
@@ -1,8 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">mothur/mothur</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest
index b9f25caf1..c0683d041 100644
--- a/sci-biology/ncbi-blast+/Manifest
+++ b/sci-biology/ncbi-blast+/Manifest
@@ -1,3 +1,3 @@
DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 SHA256 26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40 SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17 WHIRLPOOL 64f63fdf1502f3d069ffa645b378fb50469d689b70eefbbc85e04bbe4ae896d1e4dfc860a81e2d7c27bc9484eb6a9651ac02ee1d712b9a511d33a9be241154e9
DIST ncbi-blast-2.2.31+-src.tar.gz 18971327 SHA256 f0960e8af2a6021fde6f2513381493641f687453a804239a7e598649b432f8a5 SHA512 2681a4394cc250d1ee545cd85dc962d73b1dbbdd987790a029bf51a58e74cbb08b5c8cf4a02b9b7c95916e3fb0d1613e2ed8631bb7ad683156759421081bb4ca WHIRLPOOL 65e93f87d4c48d8c44cf90c672bdb2035ddb960a388d46f6438c113972392ac23ec0b859a4ecf9c3493c4ee7739dc1f54e545f2758aa889c61d0d95ef9f0a173
-DIST ncbi-blast-2.3.0+-src.tar.gz 19233464 SHA256 7ce8dc62f58141b6cdcd56b55ea3c17bea7a672e6256dfd725e6ef94825e94e9 SHA512 de1002eecf062f3cae61eaec5561a7d8a6118dbcaf243899421a49ebd98f1f7aa54b86d7478445ff6109b0b09645d4969a6ce947a968093d92c41c335ec1c600 WHIRLPOOL 6cec5490251701d8e1e5200144eaa22bfaaa110499b143c832d8f86daf34d214f9871566e65767a44e66fef0b95c01f43a6ab02b985e5b6c3bf25dc3d4a7d3ae
+DIST ncbi-blast-2.6.0+-src.tar.gz 20025526 SHA256 0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996 SHA512 ea6444892a0b10459193d33d243b5960ad206b702e01e94a554a5ebda0291ff45e1ce43479713c23a96eba676b40bb8c57a7ef9dd2118729feef6b2cd98560c6 WHIRLPOOL 1283f8b6eb04e910245963bc2931d2de88bc21128266c28c16ed65b8365e0b12909d3395035c0cf7a19ee7924cea4facc1dd3246175f10dd5e64dcb12a1061a3
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 7791cf3e5..6adbefad3 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.3.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -239,7 +239,9 @@ src_configure() {
$(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
- $(use_with opengl glew-mx)
+ #
+ # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302
+ # $(use_with opengl glew-mx)
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
@@ -264,6 +266,8 @@ src_configure() {
$(use_with curl curl "${EPREFIX}/usr")
# $(use_with X x "${EPREFIX}/usr")
# $(use_with X x) # there is no --with-x option
+ # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution
+ --without-vdb
)
# http://www.ncbi.nlm.nih.gov/books/NBK7167/
diff --git a/sci-biology/nilearn/metadata.xml b/sci-biology/nilearn/metadata.xml
index 7fee88bbe..3954d1f57 100644
--- a/sci-biology/nilearn/metadata.xml
+++ b/sci-biology/nilearn/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -19,5 +19,6 @@
</use>
<upstream>
<remote-id type="pypi">nilearn</remote-id>
+ <remote-id type="github">nilearn/nilearn</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/nwalign/metadata.xml b/sci-biology/nwalign/metadata.xml
index 1699e58b2..d5c7b72f2 100644
--- a/sci-biology/nwalign/metadata.xml
+++ b/sci-biology/nwalign/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="pypi">nwalign</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/nxtrim/metadata.xml b/sci-biology/nxtrim/metadata.xml
index f68a1b6fa..b4b118dab 100644
--- a/sci-biology/nxtrim/metadata.xml
+++ b/sci-biology/nxtrim/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">sequencing/NxTrim</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/oncotator/metadata.xml b/sci-biology/oncotator/metadata.xml
index f68a1b6fa..4f2a2f45a 100644
--- a/sci-biology/oncotator/metadata.xml
+++ b/sci-biology/oncotator/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">broadinstitute/oncotator</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/perga/metadata.xml b/sci-biology/perga/metadata.xml
index f68a1b6fa..be641f1a0 100644
--- a/sci-biology/perga/metadata.xml
+++ b/sci-biology/perga/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">hitbio/PERGA</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml
index 1699e58b2..d0f646374 100644
--- a/sci-biology/phusion2/metadata.xml
+++ b/sci-biology/phusion2/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">downloads</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
index 513e8631c..4ec209225 100644
--- a/sci-biology/picard/metadata.xml
+++ b/sci-biology/picard/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">picard</remote-id>
+ <remote-id type="github">broadinstitute/picard</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/prinseq-lite/metadata.xml b/sci-biology/prinseq-lite/metadata.xml
index f68a1b6fa..d5c8298fe 100644
--- a/sci-biology/prinseq-lite/metadata.xml
+++ b/sci-biology/prinseq-lite/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">prinseq</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/psychopy/metadata.xml b/sci-biology/psychopy/metadata.xml
index c74323f81..e5d49f5cb 100644
--- a/sci-biology/psychopy/metadata.xml
+++ b/sci-biology/psychopy/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">psychpy</remote-id>
+ <remote-id type="github">psychopy/psychopy</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/pybrain/metadata.xml b/sci-biology/pybrain/metadata.xml
index 8425c0d53..0ac4c31dd 100644
--- a/sci-biology/pybrain/metadata.xml
+++ b/sci-biology/pybrain/metadata.xml
@@ -1,8 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">pybrain/pybrain</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml
index f68a1b6fa..1bd906efe 100644
--- a/sci-biology/pysamstats/metadata.xml
+++ b/sci-biology/pysamstats/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,8 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">alimanfoo/pysamstats</remote-id>
+ <remote-id type="pypi">pysamstats</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/ruffus/metadata.xml b/sci-biology/ruffus/metadata.xml
index 1699e58b2..5541360c7 100644
--- a/sci-biology/ruffus/metadata.xml
+++ b/sci-biology/ruffus/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="pypi">ruffus</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml
index f68a1b6fa..ab03f4219 100644
--- a/sci-biology/sambamba/metadata.xml
+++ b/sci-biology/sambamba/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">lomereiter/sambamba</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/scbi_blast/metadata.xml b/sci-biology/scbi_blast/metadata.xml
index 5c826014b..dd1623955 100644
--- a/sci-biology/scbi_blast/metadata.xml
+++ b/sci-biology/scbi_blast/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id>
+ <remote-id type="rubygems">scbi_blast</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/scbi_fasta/metadata.xml b/sci-biology/scbi_fasta/metadata.xml
index 5c826014b..f8f3e47a2 100644
--- a/sci-biology/scbi_fasta/metadata.xml
+++ b/sci-biology/scbi_fasta/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id>
+ <remote-id type="rubygems">scbi_fasta</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/scbi_fastq/metadata.xml b/sci-biology/scbi_fastq/metadata.xml
index f68a1b6fa..69f445f42 100644
--- a/sci-biology/scbi_fastq/metadata.xml
+++ b/sci-biology/scbi_fastq/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="rubygems">scbi_fastq</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/scbi_mapreduce/metadata.xml b/sci-biology/scbi_mapreduce/metadata.xml
index 5c826014b..a39eed183 100644
--- a/sci-biology/scbi_mapreduce/metadata.xml
+++ b/sci-biology/scbi_mapreduce/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id>
+ <remote-id type="rubygems">scbi_mapreduce</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/scbi_plot/metadata.xml b/sci-biology/scbi_plot/metadata.xml
index 5c826014b..5e2713549 100644
--- a/sci-biology/scbi_plot/metadata.xml
+++ b/sci-biology/scbi_plot/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id>
+ <remote-id type="rubygems">scbi_plot</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/scbi_zcat/metadata.xml b/sci-biology/scbi_zcat/metadata.xml
index f68a1b6fa..a55e8612a 100644
--- a/sci-biology/scbi_zcat/metadata.xml
+++ b/sci-biology/scbi_zcat/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="rubygems">scbi_zcat</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/smalt/metadata.xml b/sci-biology/smalt/metadata.xml
index 1699e58b2..4b2ca765e 100644
--- a/sci-biology/smalt/metadata.xml
+++ b/sci-biology/smalt/metadata.xml
@@ -1,12 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?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">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="sourceforge">smalt</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/snpomatic/metadata.xml b/sci-biology/snpomatic/metadata.xml
index f68a1b6fa..47ff2f6ab 100644
--- a/sci-biology/snpomatic/metadata.xml
+++ b/sci-biology/snpomatic/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">magnusmanske/snpomatic</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml
index f68a1b6fa..d931eaf33 100644
--- a/sci-biology/somatic-sniper/metadata.xml
+++ b/sci-biology/somatic-sniper/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">genome/somatic-sniper</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml
index f68a1b6fa..73d16b005 100644
--- a/sci-biology/staden_doc/metadata.xml
+++ b/sci-biology/staden_doc/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<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/stringtie/metadata.xml b/sci-biology/stringtie/metadata.xml
index f68a1b6fa..b909ea058 100644
--- a/sci-biology/stringtie/metadata.xml
+++ b/sci-biology/stringtie/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">gpertea/stringtie</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/vcflib/metadata.xml b/sci-biology/vcflib/metadata.xml
index f68a1b6fa..ce295b942 100644
--- a/sci-biology/vcflib/metadata.xml
+++ b/sci-biology/vcflib/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">vcflib/vcflib</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
index 77f6f92e0..6c22d1920 100644
--- a/sci-biology/vcftools/metadata.xml
+++ b/sci-biology/vcftools/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">vcftools</remote-id>
+ <remote-id type="github">vcftools/vcftools</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-biology/verifyBamID/metadata.xml b/sci-biology/verifyBamID/metadata.xml
index f68a1b6fa..41b69bc9c 100644
--- a/sci-biology/verifyBamID/metadata.xml
+++ b/sci-biology/verifyBamID/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">statgen/libStatGen</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/vt/metadata.xml b/sci-biology/vt/metadata.xml
index f68a1b6fa..ab18754bf 100644
--- a/sci-biology/vt/metadata.xml
+++ b/sci-biology/vt/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">atks/vt</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-biology/yaha/metadata.xml b/sci-biology/yaha/metadata.xml
index f68a1b6fa..4d610cc7e 100644
--- a/sci-biology/yaha/metadata.xml
+++ b/sci-biology/yaha/metadata.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
@@ -9,4 +9,7 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">GregoryFaust/yaha</remote-id>
+ </upstream>
</pkgmetadata>