* [gentoo-commits] proj/sci:master commit in: sci-biology/karect/, sci-chemistry/wxmacmolplt/, sci-biology/grass/, ...
@ 2017-04-29 9:50 Justin Lecher
0 siblings, 0 replies; only message in thread
From: Justin Lecher @ 2017-04-29 9:50 UTC (permalink / raw
To: gentoo-commits
commit: 61094665a0622c77dea66a04ec74b5e4fd71bb46
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 29 09:50:07 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Apr 29 09:50:24 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=61094665
Update remote ids
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
dev-java/htsjdk/metadata.xml | 3 ++-
dev-libs/opencl-clhpp/metadata.xml | 7 +++++--
dev-python/PeakUtils/metadata.xml | 3 ++-
dev-python/busfactor/metadata.xml | 3 +++
dev-python/ffnet/metadata.xml | 6 ++++--
dev-python/ffnetui/metadata.xml | 6 ++++--
dev-python/gitana/metadata.xml | 3 +++
dev-python/matplotlib-venn/metadata.xml | 3 ++-
dev-python/py2bit/metadata.xml | 5 ++++-
dev-python/pyBigWig/metadata.xml | 5 ++++-
dev-python/shove/metadata.xml | 5 ++++-
dev-python/snakemake/metadata.xml | 4 +++-
dev-util/emscripten-fastcomp/metadata.xml | 5 ++++-
dev-util/emscripten/metadata.xml | 5 ++++-
dev-util/mad-numdiff/metadata.xml | 5 ++++-
sci-biology/Fastaq/metadata.xml | 5 ++++-
sci-biology/MolBioLib/metadata.xml | 5 ++++-
sci-biology/Rcorrector/metadata.xml | 7 +++++--
sci-biology/Scaffolder-evaluation/metadata.xml | 5 ++++-
sci-biology/SnpEff/metadata.xml | 5 ++++-
sci-biology/VarScan-bin/metadata.xml | 3 ++-
sci-biology/VarScan/metadata.xml | 3 ++-
sci-biology/assembly-stats/metadata.xml | 5 ++++-
sci-biology/bam-readcount/metadata.xml | 5 ++++-
sci-biology/bfast/metadata.xml | 5 ++++-
sci-biology/bio-cd-hit-report/metadata.xml | 5 ++++-
sci-biology/cd-hit/metadata.xml | 5 +++--
sci-biology/conrad/metadata.xml | 5 ++++-
sci-biology/cramtools/metadata.xml | 5 ++++-
sci-biology/cross_genome/metadata.xml | 5 ++++-
sci-biology/cutadapt/metadata.xml | 3 ++-
sci-biology/deeptools/metadata.xml | 5 ++++-
sci-biology/ensembl-tools/metadata.xml | 5 ++++-
sci-biology/fgap-bin/metadata.xml | 5 ++++-
sci-biology/fgap/metadata.xml | 5 ++++-
sci-biology/flexbar/metadata.xml | 3 ++-
sci-biology/gemini/metadata.xml | 5 ++++-
sci-biology/grabix/metadata.xml | 5 ++++-
sci-biology/grass/metadata.xml | 7 +++++--
sci-biology/hisat2/metadata.xml | 5 ++++-
sci-biology/hts-python/metadata.xml | 5 ++++-
sci-biology/jannovar-bin/metadata.xml | 7 +++++--
sci-biology/jannovar/metadata.xml | 5 ++++-
sci-biology/jtreeview-bin/metadata.xml | 5 ++++-
sci-biology/jtreeview/metadata.xml | 3 ++-
sci-biology/karect/metadata.xml | 5 ++++-
sci-biology/kat/metadata.xml | 5 ++++-
sci-biology/libBigWig/metadata.xml | 5 ++++-
sci-biology/lumpy-sv/metadata.xml | 5 ++++-
sci-biology/megahit/metadata.xml | 5 ++++-
sci-biology/mothur/metadata.xml | 5 ++++-
sci-biology/nilearn/metadata.xml | 3 ++-
sci-biology/nwalign/metadata.xml | 7 +++++--
sci-biology/nxtrim/metadata.xml | 5 ++++-
sci-biology/oncotator/metadata.xml | 5 ++++-
sci-biology/perga/metadata.xml | 5 ++++-
sci-biology/phusion2/metadata.xml | 7 +++++--
sci-biology/picard/metadata.xml | 3 ++-
sci-biology/prinseq-lite/metadata.xml | 5 ++++-
sci-biology/psychopy/metadata.xml | 3 ++-
sci-biology/pybrain/metadata.xml | 5 ++++-
sci-biology/pysamstats/metadata.xml | 6 +++++-
sci-biology/ruffus/metadata.xml | 7 +++++--
sci-biology/sambamba/metadata.xml | 5 ++++-
sci-biology/scbi_blast/metadata.xml | 3 ++-
sci-biology/scbi_fasta/metadata.xml | 3 ++-
sci-biology/scbi_fastq/metadata.xml | 5 ++++-
sci-biology/scbi_mapreduce/metadata.xml | 3 ++-
sci-biology/scbi_plot/metadata.xml | 3 ++-
sci-biology/scbi_zcat/metadata.xml | 5 ++++-
sci-biology/smalt/metadata.xml | 7 +++++--
sci-biology/snpomatic/metadata.xml | 5 ++++-
sci-biology/somatic-sniper/metadata.xml | 5 ++++-
sci-biology/staden_doc/metadata.xml | 5 ++++-
sci-biology/stringtie/metadata.xml | 5 ++++-
sci-biology/vcflib/metadata.xml | 5 ++++-
sci-biology/vcftools/metadata.xml | 3 ++-
sci-biology/verifyBamID/metadata.xml | 5 ++++-
sci-biology/vt/metadata.xml | 5 ++++-
sci-biology/yaha/metadata.xml | 5 ++++-
sci-chemistry/wxmacmolplt/metadata.xml | 5 ++++-
sci-libs/arrayfire/metadata.xml | 5 ++++-
sci-libs/bloom/metadata.xml | 7 +++++--
sci-libs/dtk/metadata.xml | 3 +++
sci-libs/lib2bit/metadata.xml | 5 ++++-
sci-libs/libStatGen/metadata.xml | 5 ++++-
sci-libs/lmfit/metadata.xml | 5 ++++-
sci-libs/nexus/metadata.xml | 5 ++++-
sci-libs/nipype/metadata.xml | 3 ++-
sci-libs/pmx/metadata.xml | 5 ++++-
sci-libs/shtools/metadata.xml | 5 ++++-
sci-mathematics/dolfin/metadata.xml | 11 ++++++-----
sci-mathematics/mathics/metadata.xml | 5 ++++-
sci-mathematics/tisean/metadata.xml | 5 ++++-
sci-misc/mitlm/metadata.xml | 7 +++++--
95 files changed, 354 insertions(+), 109 deletions(-)
diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml
index 513e8631c..6c001f352 100644
--- a/dev-java/htsjdk/metadata.xml
+++ b/dev-java/htsjdk/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">samtools/htsjdk</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-libs/opencl-clhpp/metadata.xml b/dev-libs/opencl-clhpp/metadata.xml
index 222c1e307..5ef422065 100644
--- a/dev-libs/opencl-clhpp/metadata.xml
+++ b/dev-libs/opencl-clhpp/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@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
-</pkgmetadata>
\ No newline at end of file
+ <upstream>
+ <remote-id type="github">KhronosGroup/OpenCL-CLHPP</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/PeakUtils/metadata.xml b/dev-python/PeakUtils/metadata.xml
index c39ab9b4e..a4c17d458 100644
--- a/dev-python/PeakUtils/metadata.xml
+++ b/dev-python/PeakUtils/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">
@@ -14,5 +14,6 @@
</longdescription>
<upstream>
<remote-id type="pypi">PeakUtils</remote-id>
+ <remote-id type="bitbucket">lucashnegri/peakutils</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/busfactor/metadata.xml b/dev-python/busfactor/metadata.xml
index ec9fa9d47..edbc63649 100644
--- a/dev-python/busfactor/metadata.xml
+++ b/dev-python/busfactor/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">SOM-Research/busfactor</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/ffnet/metadata.xml b/dev-python/ffnet/metadata.xml
index e40054cae..81dcc789e 100644
--- a/dev-python/ffnet/metadata.xml
+++ b/dev-python/ffnet/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">
@@ -8,11 +8,13 @@
<longdescription lang="en">
ffnet is a fast and easy-to-use feed-forward neural
network training library for python.
-</longdescription>
+ </longdescription>
<use>
<flag name="matplotlib">Use matplotlib for drawing</flag>
</use>
<upstream>
<remote-id type="github">mrkwjc/ffnet</remote-id>
+ <remote-id type="pypi">ffnet</remote-id>
+ <remote-id type="sourceforge">ffnet</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/ffnetui/metadata.xml b/dev-python/ffnetui/metadata.xml
index 6e1e5f91c..50cd8d0c5 100644
--- a/dev-python/ffnetui/metadata.xml
+++ b/dev-python/ffnetui/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">
@@ -7,8 +7,10 @@
</maintainer>
<longdescription lang="en">
GUI for ffnet - feed forward neural network for python
-</longdescription>
+ </longdescription>
<upstream>
<remote-id type="github">mrkwjc/ffnetui</remote-id>
+ <remote-id type="pypi">ffnetui</remote-id>
+ <remote-id type="sourceforge">ffnet</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/gitana/metadata.xml b/dev-python/gitana/metadata.xml
index ec9fa9d47..221a98348 100644
--- a/dev-python/gitana/metadata.xml
+++ b/dev-python/gitana/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">SOM-Research/gitana</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/matplotlib-venn/metadata.xml b/dev-python/matplotlib-venn/metadata.xml
index 01447d81f..8401ce8b5 100644
--- a/dev-python/matplotlib-venn/metadata.xml
+++ b/dev-python/matplotlib-venn/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="github">matplotlib-venn</remote-id>
+ <remote-id type="pypi">matplotlib-venn</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-python/py2bit/metadata.xml b/dev-python/py2bit/metadata.xml
index f68a1b6fa..71d7d5a6a 100644
--- a/dev-python/py2bit/metadata.xml
+++ b/dev-python/py2bit/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/py2bit</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml
index f68a1b6fa..764884a58 100644
--- a/dev-python/pyBigWig/metadata.xml
+++ b/dev-python/pyBigWig/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/pyBigWig</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/shove/metadata.xml b/dev-python/shove/metadata.xml
index f68a1b6fa..a5faa4b26 100644
--- a/dev-python/shove/metadata.xml
+++ b/dev-python/shove/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">lcrees/shove</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml
index 63e701edd..9fb8f07d6 100644
--- a/dev-python/snakemake/metadata.xml
+++ b/dev-python/snakemake/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 +11,7 @@
</maintainer>
<upstream>
<remote-id type="github">dev-python/snakemake</remote-id>
+ <remote-id type="bitbucket">johanneskoester/snakemake</remote-id>
+ <remote-id type="pypi">snakemake</remote-id>
</upstream>
</pkgmetadata>
diff --git a/dev-util/emscripten-fastcomp/metadata.xml b/dev-util/emscripten-fastcomp/metadata.xml
index d9e70962e..ee38ab80a 100644
--- a/dev-util/emscripten-fastcomp/metadata.xml
+++ b/dev-util/emscripten-fastcomp/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="person">
<email>harald.weiner@jku.at</email>
<name>Harald Weiner</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">kripken/emscripten-fastcomp-clang</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-util/emscripten/metadata.xml b/dev-util/emscripten/metadata.xml
index d9e70962e..bbd406949 100644
--- a/dev-util/emscripten/metadata.xml
+++ b/dev-util/emscripten/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="person">
<email>harald.weiner@jku.at</email>
<name>Harald Weiner</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">kripken/emscripten</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-util/mad-numdiff/metadata.xml b/dev-util/mad-numdiff/metadata.xml
index 7ec6883d7..729575510 100644
--- a/dev-util/mad-numdiff/metadata.xml
+++ b/dev-util/mad-numdiff/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-physics@gentoo.org</email>
<name>Gentoo Physics Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">quinoacomputing/ndiff</remote-id>
+ </upstream>
</pkgmetadata>
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/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/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>
diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml
index 19df98469..fa784e844 100644
--- a/sci-chemistry/wxmacmolplt/metadata.xml
+++ b/sci-chemistry/wxmacmolplt/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">
@@ -17,4 +17,7 @@
Add support for flash movie generation using <pkg>media-libs/ming</pkg>
</flag>
</use>
+ <upstream>
+ <remote-id type="github">brettbode/wxmacmolplt</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/arrayfire/metadata.xml b/sci-libs/arrayfire/metadata.xml
index 9903267a4..994d7bb3d 100644
--- a/sci-libs/arrayfire/metadata.xml
+++ b/sci-libs/arrayfire/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">
@@ -36,4 +36,7 @@
Build Backend-Independent API.
</flag>
</use>
+ <upstream>
+ <remote-id type="github">google/googletest</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/bloom/metadata.xml b/sci-libs/bloom/metadata.xml
index 1699e58b2..ea4817fa3 100644
--- a/sci-libs/bloom/metadata.xml
+++ b/sci-libs/bloom/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">arashpartow/bloom</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/dtk/metadata.xml b/sci-libs/dtk/metadata.xml
index ec9fa9d47..92ff8e86b 100644
--- a/sci-libs/dtk/metadata.xml
+++ b/sci-libs/dtk/metadata.xml
@@ -9,4 +9,7 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">d-tk/dtk</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/lib2bit/metadata.xml b/sci-libs/lib2bit/metadata.xml
index f68a1b6fa..1f37ac0f9 100644
--- a/sci-libs/lib2bit/metadata.xml
+++ b/sci-libs/lib2bit/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/lib2bit</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/libStatGen/metadata.xml b/sci-libs/libStatGen/metadata.xml
index f68a1b6fa..41b69bc9c 100644
--- a/sci-libs/libStatGen/metadata.xml
+++ b/sci-libs/libStatGen/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-libs/lmfit/metadata.xml b/sci-libs/lmfit/metadata.xml
index 8425c0d53..a4573ac05 100644
--- a/sci-libs/lmfit/metadata.xml
+++ b/sci-libs/lmfit/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="sourceforge">lmfit</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/nexus/metadata.xml b/sci-libs/nexus/metadata.xml
index 4ef50910d..901161d45 100644
--- a/sci-libs/nexus/metadata.xml
+++ b/sci-libs/nexus/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">
@@ -23,4 +23,7 @@
<flag name="java">Build the Java bindings</flag>
<flag name="utils">Build optional utility applications</flag>
</use>
+ <upstream>
+ <remote-id type="github">nexusformat/code</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/nipype/metadata.xml b/sci-libs/nipype/metadata.xml
index c9064b1ae..8e5a54081 100644
--- a/sci-libs/nipype/metadata.xml
+++ b/sci-libs/nipype/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">
@@ -23,5 +23,6 @@
</longdescription>
<upstream>
<remote-id type="sourceforge">nipy</remote-id>
+ <remote-id type="github">nipy/nipype</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-libs/pmx/metadata.xml b/sci-libs/pmx/metadata.xml
index 988041704..cb2e5209a 100644
--- a/sci-libs/pmx/metadata.xml
+++ b/sci-libs/pmx/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">
@@ -13,4 +13,7 @@
functionalities, e.g. gromacs file parsers and scripts for setup and
analysis of free energy calculations.
</longdescription>
+ <upstream>
+ <remote-id type="github">dseeliger/pmx</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-libs/shtools/metadata.xml b/sci-libs/shtools/metadata.xml
index bacae8d93..518b8e2dd 100644
--- a/sci-libs/shtools/metadata.xml
+++ b/sci-libs/shtools/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">
@@ -15,4 +15,7 @@
reconstructions, rotations of data expressed in spherical
harmonics, and multitaper spectral analyses on the sphere.
</longdescription>
+ <upstream>
+ <remote-id type="github">SHTOOLS/SHTOOLS</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-mathematics/dolfin/metadata.xml b/sci-mathematics/dolfin/metadata.xml
index 70a8a021f..c45db3d3e 100644
--- a/sci-mathematics/dolfin/metadata.xml
+++ b/sci-mathematics/dolfin/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">
@@ -7,19 +7,20 @@
</maintainer>
<longdescription lang="en">
DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.
-</longdescription>
+ </longdescription>
<use>
<flag name="cgal">Adds support for geometric algorithms with <pkg>sci-mathematics/cgal</pkg></flag>
<flag name="cholmod">Adds support for sparse Cholesky factorization with <pkg>sci-libs/cholmod</pkg></flag>
- <flag name="hdf5">Adds support for <pkg>sci-libs/hdf5</pkg></flag>
+ <flag name="hdf5">Adds support for <pkg>sci-libs/hdf5</pkg></flag>
<flag name="parmetis">Adds support for parallel graph partitioning with <pkg>sci-libs/parmetis</pkg></flag>
- <flag name="petsc">Adds support for numerical linear algebra toolkit <pkg>sci-mathematics/petsc</pkg></flag>
+ <flag name="petsc">Adds support for numerical linear algebra toolkit <pkg>sci-mathematics/petsc</pkg></flag>
<flag name="scotch">Adds support for graph partitioning with <pkg>sci-libs/scotch</pkg></flag>
- <flag name="trilinos">Adds support for numerical linear algebra toolkit <pkg>sci-libs/trilinos</pkg></flag>
+ <flag name="trilinos">Adds support for numerical linear algebra toolkit <pkg>sci-libs/trilinos</pkg></flag>
<flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag>
<flag name="vtk">Adds support for the visualization toolkit <pkg>sci-libs/vtk</pkg></flag>
</use>
<upstream>
<remote-id type="launchpad">dolfin</remote-id>
+ <remote-id type="bitbucket">fenics-project/dolfin</remote-id>
</upstream>
</pkgmetadata>
diff --git a/sci-mathematics/mathics/metadata.xml b/sci-mathematics/mathics/metadata.xml
index 9cb351fa7..d2e5a63b0 100644
--- a/sci-mathematics/mathics/metadata.xml
+++ b/sci-mathematics/mathics/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">
@@ -18,4 +18,7 @@
However, Mathics is in no way affiliated or supported by Wolfram. Mathics will probably never have the power to
compete with Mathematica® in industrial applications; yet, it might be an interesting alternative for educational purposes.
</longdescription>
+ <upstream>
+ <remote-id type="github">mathics/Mathics</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml
index 3be7b5248..04bcf9b8c 100644
--- a/sci-mathematics/tisean/metadata.xml
+++ b/sci-mathematics/tisean/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="person">
<email>jlec@gentoo.org</email>
<name>Justin Lecher (jlec)</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">heggus/Tisean</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-misc/mitlm/metadata.xml b/sci-misc/mitlm/metadata.xml
index 5e38f5236..05123bc6e 100644
--- a/sci-misc/mitlm/metadata.xml
+++ b/sci-misc/mitlm/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">
@@ -9,6 +9,9 @@
designed for the efficient estimation of statistical n-gram
language models involving iterative parameter estimation.
It achieves much of its efficiency through the use of a compact
- vector representation of n-grams.
+ vector representation of n-grams.
</longdescription>
+ <upstream>
+ <remote-id type="github">mitlm/mitlm</remote-id>
+ </upstream>
</pkgmetadata>
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