Add upstream remote-id annotations using tools by Corentin Chary, bug #406287.

10 files changed, 39 insertions, 12 deletions

diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
index dffdf8b00408..7f04ab3240d0 100644
--- a/sci-biology/bedtools/metadata.xml
+++ b/sci-biology/bedtools/metadata.xml
@@ -11,4 +11,7 @@
 		<name>Martin Mokrejs</name>
 	</maintainer>
 	<longdescription>BEDTools: a flexible suite of utilities for comparing genomic features.</longdescription>
+	<upstream>
+		<remote-id type="google-code">bedtools</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml
index 3302123e5718..e135d348a383 100644
--- a/sci-biology/bioperl-db/metadata.xml
+++ b/sci-biology/bioperl-db/metadata.xml
@@ -6,4 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="cpan">bioperl-db</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml
index 3302123e5718..2cc65a78a60a 100644
--- a/sci-biology/bioperl-network/metadata.xml
+++ b/sci-biology/bioperl-network/metadata.xml
@@ -6,4 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="cpan">bioperl-network</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml
index d4648212cbad..472edcc70b95 100644
--- a/sci-biology/bioperl-run/metadata.xml
+++ b/sci-biology/bioperl-run/metadata.xml
@@ -2,4 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="cpan">bioperl-run</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
index abf6b4cdce48..9cb32209f148 100644
--- a/sci-biology/bioperl/metadata.xml
+++ b/sci-biology/bioperl/metadata.xml
@@ -3,8 +3,11 @@
 <pkgmetadata>
 	<herd>sci-biology</herd>
 	<use>
-		<flag name='run'>Install sci-biology/bioperl-run</flag>
-		<flag name='network'>Install sci-biology/bioperl-run</flag>
-		<flag name='db'>Install sci-biology/bioperl-run</flag>
+		<flag name="run">Install sci-biology/bioperl-run</flag>
+		<flag name="network">Install sci-biology/bioperl-run</flag>
+		<flag name="db">Install sci-biology/bioperl-run</flag>
 	</use>
+	<upstream>
+		<remote-id type="cpan">bioperl</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
index 0066dc245f77..e4184a444391 100644
--- a/sci-biology/cd-hit/metadata.xml
+++ b/sci-biology/cd-hit/metadata.xml
@@ -1,17 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
-<longdescription>
-CD-HIT is a very widely used program for clustering and comparing large sets 
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
+	<longdescription>CD-HIT is a very widely used program for clustering and comparing large sets 
 of protein or nucleotide sequences. CD-HIT is very fast and can handle 
 extremely large databases. CD-HIT helps to significantly reduce the 
 computational and manual efforts in many sequence analysis tasks and aids in 
 understanding the data structure and correct the bias within a dataset.
-
 The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
 CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
 (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
@@ -19,6 +17,8 @@ user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2
 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>
+scripts can be found in CD-HIT user's guide.</longdescription>
+	<upstream>
+		<remote-id type="google-code">cdhit</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
index 3302123e5718..02b33ae51491 100644
--- a/sci-biology/mosaik/metadata.xml
+++ b/sci-biology/mosaik/metadata.xml
@@ -6,4 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="google-code">mosaik-aligner</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml
index 3302123e5718..919a54748e3f 100644
--- a/sci-biology/prank/metadata.xml
+++ b/sci-biology/prank/metadata.xml
@@ -6,4 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="google-code">prank-msa</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml
index d4648212cbad..6e8b2ee66e66 100644
--- a/sci-biology/prodigal/metadata.xml
+++ b/sci-biology/prodigal/metadata.xml
@@ -2,4 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="google-code">prodigal</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
index 3302123e5718..7743d6190a21 100644
--- a/sci-biology/pysam/metadata.xml
+++ b/sci-biology/pysam/metadata.xml
@@ -6,4 +6,7 @@
 		<name>Andrey Kislyuk</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<upstream>
+		<remote-id type="google-code">pysam</remote-id>
+	</upstream>
 </pkgmetadata>