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Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/ApE/metadata.xml2
-rw-r--r--sci-biology/GBrowse/metadata.xml2
-rw-r--r--sci-biology/aaindex/metadata.xml2
-rw-r--r--sci-biology/abyss/metadata.xml2
-rw-r--r--sci-biology/allpathslg/metadata.xml2
-rw-r--r--sci-biology/amap/metadata.xml2
-rw-r--r--sci-biology/amos/metadata.xml2
-rw-r--r--sci-biology/arb/arb-5.1-r1.ebuild2
-rw-r--r--sci-biology/arb/arb-5.2.ebuild2
-rw-r--r--sci-biology/arb/arb-5.3.ebuild2
-rw-r--r--sci-biology/arb/metadata.xml2
-rw-r--r--sci-biology/ariadne/metadata.xml2
-rw-r--r--sci-biology/augustus/metadata.xml2
-rw-r--r--sci-biology/bamtools/metadata.xml2
-rw-r--r--sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild2
-rw-r--r--sci-biology/beast-mcmc/metadata.xml2
-rw-r--r--sci-biology/bedtools/metadata.xml2
-rw-r--r--sci-biology/bfast/metadata.xml2
-rw-r--r--sci-biology/biogrep/metadata.xml2
-rw-r--r--sci-biology/biojava/metadata.xml2
-rw-r--r--sci-biology/bioperl-db/metadata.xml2
-rw-r--r--sci-biology/bioperl-network/metadata.xml2
-rw-r--r--sci-biology/bioperl-run/metadata.xml2
-rw-r--r--sci-biology/bioperl/metadata.xml2
-rw-r--r--sci-biology/biopython/metadata.xml2
-rw-r--r--sci-biology/bioruby/metadata.xml2
-rw-r--r--sci-biology/biosql/metadata.xml2
-rw-r--r--sci-biology/blat/metadata.xml2
-rw-r--r--sci-biology/blossoc/metadata.xml2
-rw-r--r--sci-biology/bowtie/metadata.xml2
-rw-r--r--sci-biology/bwa/metadata.xml2
-rw-r--r--sci-biology/cd-hit/metadata.xml2
-rw-r--r--sci-biology/clustal-omega/metadata.xml2
-rw-r--r--sci-biology/clustalw-mpi/metadata.xml2
-rw-r--r--sci-biology/clustalw/metadata.xml2
-rw-r--r--sci-biology/clustalx/metadata.xml2
-rw-r--r--sci-biology/consed/metadata.xml2
-rw-r--r--sci-biology/cufflinks/metadata.xml2
-rw-r--r--sci-biology/cutg/cutg-160-r1.ebuild2
-rw-r--r--sci-biology/cutg/metadata.xml2
-rw-r--r--sci-biology/dialign-tx/metadata.xml2
-rw-r--r--sci-biology/dialign2/metadata.xml2
-rw-r--r--sci-biology/diya/metadata.xml2
-rw-r--r--sci-biology/elph/metadata.xml2
-rw-r--r--sci-biology/embassy-cbstools/metadata.xml2
-rw-r--r--sci-biology/embassy-clustalomega/metadata.xml2
-rw-r--r--sci-biology/embassy-domainatrix/metadata.xml2
-rw-r--r--sci-biology/embassy-domalign/metadata.xml2
-rw-r--r--sci-biology/embassy-domsearch/metadata.xml2
-rw-r--r--sci-biology/embassy-emnu/metadata.xml2
-rw-r--r--sci-biology/embassy-esim4/metadata.xml2
-rw-r--r--sci-biology/embassy-hmmer/metadata.xml2
-rw-r--r--sci-biology/embassy-iprscan/metadata.xml2
-rw-r--r--sci-biology/embassy-meme/metadata.xml2
-rw-r--r--sci-biology/embassy-memenew/metadata.xml2
-rw-r--r--sci-biology/embassy-mira/metadata.xml2
-rw-r--r--sci-biology/embassy-mse/metadata.xml2
-rw-r--r--sci-biology/embassy-phylipnew/metadata.xml2
-rw-r--r--sci-biology/embassy-signature/metadata.xml2
-rw-r--r--sci-biology/embassy-structure/metadata.xml2
-rw-r--r--sci-biology/embassy-topo/metadata.xml2
-rw-r--r--sci-biology/embassy-vienna/metadata.xml2
-rw-r--r--sci-biology/embassy/metadata.xml2
-rw-r--r--sci-biology/emboss/metadata.xml2
-rw-r--r--sci-biology/eugene/metadata.xml2
-rw-r--r--sci-biology/exonerate/metadata.xml2
-rw-r--r--sci-biology/express/metadata.xml2
-rw-r--r--sci-biology/fasta/metadata.xml2
-rw-r--r--sci-biology/fasttree/metadata.xml2
-rw-r--r--sci-biology/finchtv/metadata.xml2
-rw-r--r--sci-biology/flower/metadata.xml2
-rw-r--r--sci-biology/foldingathome/metadata.xml2
-rw-r--r--sci-biology/gatk/metadata.xml2
-rw-r--r--sci-biology/gibbs/metadata.xml2
-rw-r--r--sci-biology/glimmer/metadata.xml2
-rw-r--r--sci-biology/glimmerhmm/metadata.xml2
-rw-r--r--sci-biology/gmap/metadata.xml2
-rw-r--r--sci-biology/goby-cpp/metadata.xml2
-rw-r--r--sci-biology/goby/metadata.xml2
-rw-r--r--sci-biology/hmmer/metadata.xml2
-rw-r--r--sci-biology/iedera/metadata.xml2
-rw-r--r--sci-biology/infernal/metadata.xml2
-rw-r--r--sci-biology/iqpnni/metadata.xml2
-rw-r--r--sci-biology/kalign/metadata.xml2
-rw-r--r--sci-biology/lagan/metadata.xml2
-rw-r--r--sci-biology/last/metadata.xml2
-rw-r--r--sci-biology/mafft/metadata.xml2
-rw-r--r--sci-biology/mammoth/metadata.xml2
-rw-r--r--sci-biology/maq/metadata.xml2
-rw-r--r--sci-biology/maqview/metadata.xml2
-rw-r--r--sci-biology/mauve/metadata.xml2
-rw-r--r--sci-biology/mauvealigner/metadata.xml2
-rw-r--r--sci-biology/mcl/metadata.xml2
-rw-r--r--sci-biology/meme/metadata.xml2
-rw-r--r--sci-biology/metadata.xml2
-rw-r--r--sci-biology/mira/metadata.xml2
-rw-r--r--sci-biology/mosaik/metadata.xml2
-rw-r--r--sci-biology/mothur/metadata.xml2
-rw-r--r--sci-biology/mrbayes/metadata.xml2
-rw-r--r--sci-biology/mummer/metadata.xml2
-rw-r--r--sci-biology/muscle/metadata.xml2
-rw-r--r--sci-biology/ncbi-tools/metadata.xml2
-rw-r--r--sci-biology/newick-utils/metadata.xml2
-rw-r--r--sci-biology/njplot/metadata.xml2
-rw-r--r--sci-biology/pals/metadata.xml2
-rw-r--r--sci-biology/paml/metadata.xml2
-rw-r--r--sci-biology/phrap/metadata.xml2
-rw-r--r--sci-biology/phred/metadata.xml2
-rw-r--r--sci-biology/phylip/metadata.xml2
-rw-r--r--sci-biology/phyml/metadata.xml2
-rw-r--r--sci-biology/picard/metadata.xml2
-rw-r--r--sci-biology/picard/picard-1.103.ebuild2
-rw-r--r--sci-biology/piler/metadata.xml2
-rw-r--r--sci-biology/pilercr/metadata.xml2
-rw-r--r--sci-biology/plink/metadata.xml2
-rw-r--r--sci-biology/poa/metadata.xml2
-rw-r--r--sci-biology/prank/metadata.xml2
-rw-r--r--sci-biology/primer3/metadata.xml2
-rw-r--r--sci-biology/prints/metadata.xml2
-rw-r--r--sci-biology/probcons/metadata.xml2
-rw-r--r--sci-biology/prodigal/metadata.xml2
-rw-r--r--sci-biology/profphd/metadata.xml2
-rw-r--r--sci-biology/prosite/metadata.xml2
-rw-r--r--sci-biology/psipred/metadata.xml2
-rw-r--r--sci-biology/pysam/metadata.xml2
-rw-r--r--sci-biology/qrna/metadata.xml2
-rw-r--r--sci-biology/raxml/metadata.xml2
-rw-r--r--sci-biology/readseq/metadata.xml2
-rw-r--r--sci-biology/readseq/readseq-20080420-r1.ebuild2
-rw-r--r--sci-biology/readseq/readseq-20100513.ebuild2
-rw-r--r--sci-biology/rebase/metadata.xml2
-rw-r--r--sci-biology/rebase/rebase-1507.ebuild2
-rw-r--r--sci-biology/rebase/rebase-1508.ebuild2
-rw-r--r--sci-biology/recon/metadata.xml2
-rw-r--r--sci-biology/repeatmasker-libraries/metadata.xml2
-rw-r--r--sci-biology/repeatmasker/metadata.xml2
-rw-r--r--sci-biology/rmblast/metadata.xml2
-rw-r--r--sci-biology/rnaview/metadata.xml2
-rw-r--r--sci-biology/samtools/metadata.xml2
-rw-r--r--sci-biology/seaview/metadata.xml2
-rw-r--r--sci-biology/seqan/metadata.xml2
-rw-r--r--sci-biology/shrimp/metadata.xml2
-rw-r--r--sci-biology/sibsim4/metadata.xml2
-rw-r--r--sci-biology/sim4/metadata.xml2
-rw-r--r--sci-biology/snpfile/metadata.xml2
-rw-r--r--sci-biology/stride/metadata.xml2
-rw-r--r--sci-biology/stride/stride-20011129-r1.ebuild2
-rw-r--r--sci-biology/t-coffee/metadata.xml2
-rw-r--r--sci-biology/tophat/metadata.xml2
-rw-r--r--sci-biology/transfac/metadata.xml2
-rw-r--r--sci-biology/tree-puzzle/metadata.xml2
-rw-r--r--sci-biology/treeviewx/metadata.xml2
-rw-r--r--sci-biology/trf/metadata.xml2
-rw-r--r--sci-biology/trnascan-se/metadata.xml2
-rw-r--r--sci-biology/uchime/metadata.xml2
-rw-r--r--sci-biology/ucsc-genome-browser/metadata.xml2
-rw-r--r--sci-biology/unafold/metadata.xml2
-rw-r--r--sci-biology/update-blastdb/metadata.xml2
-rw-r--r--sci-biology/vaal/metadata.xml2
-rw-r--r--sci-biology/vcftools/metadata.xml2
-rw-r--r--sci-biology/velvet/metadata.xml2
-rw-r--r--sci-biology/vienna-rna/metadata.xml2
-rw-r--r--sci-biology/wgs-assembler/metadata.xml2
-rw-r--r--sci-biology/wise/metadata.xml2
-rw-r--r--sci-biology/yass/metadata.xml2
165 files changed, 165 insertions, 165 deletions
diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml
index 4252fbfae02..093ae3fde3e 100644
--- a/sci-biology/ApE/metadata.xml
+++ b/sci-biology/ApE/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer>
<email>je_fro@gentoo.org</email>
diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml
index 32b15c723f9..0f0451e324e 100644
--- a/sci-biology/GBrowse/metadata.xml
+++ b/sci-biology/GBrowse/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml
index ccb567e64e0..4829597f3fa 100644
--- a/sci-biology/aaindex/metadata.xml
+++ b/sci-biology/aaindex/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/abyss/metadata.xml
+++ b/sci-biology/abyss/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/allpathslg/metadata.xml
+++ b/sci-biology/allpathslg/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml
index 34294c65ca0..7a5b00148b3 100644
--- a/sci-biology/amap/metadata.xml
+++ b/sci-biology/amap/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
index a73ee9189a9..661f1f979a3 100644
--- a/sci-biology/amos/metadata.xml
+++ b/sci-biology/amos/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
index 7db2d798ec5..ed0937aed6e 100644
--- a/sci-biology/arb/arb-5.1-r1.ebuild
+++ b/sci-biology/arb/arb-5.1-r1.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="http://www.arb-home.de/"
SRC_URI="
http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
mirror://gentoo/${P}-glibc2.10.patch.bz2
- http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
+ https://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
LICENSE="arb"
SLOT="0"
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
index 97f7dc5dfbd..9c33732dc92 100644
--- a/sci-biology/arb/arb-5.2.ebuild
+++ b/sci-biology/arb/arb-5.2.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phy
HOMEPAGE="http://www.arb-home.de/"
SRC_URI="
http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
- http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"
+ https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"
SLOT="0"
LICENSE="arb"
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
index 97f8b78ddca..b0a05db2ce8 100644
--- a/sci-biology/arb/arb-5.3.ebuild
+++ b/sci-biology/arb/arb-5.3.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phy
HOMEPAGE="http://www.arb-home.de/"
SRC_URI="
http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
- http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
+ https://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
SLOT="0"
LICENSE="arb"
diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/arb/metadata.xml
+++ b/sci-biology/arb/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml
index 3e55c00f9d7..6a0a4590887 100644
--- a/sci-biology/ariadne/metadata.xml
+++ b/sci-biology/ariadne/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/augustus/metadata.xml
+++ b/sci-biology/augustus/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml
index f2c00c1fdd0..1a68503bdc8 100644
--- a/sci-biology/bamtools/metadata.xml
+++ b/sci-biology/bamtools/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<herd>proxy-maintainers</herd>
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
index 35993562814..87f177cd7de 100644
--- a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
@@ -20,7 +20,7 @@ MY_P=BEASTv${PV}
DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
HOMEPAGE="http://code.google.com/p/beast-mcmc/"
#SRC_URI=""
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
LICENSE="LGPL-3"
SLOT="0"
diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/beast-mcmc/metadata.xml
+++ b/sci-biology/beast-mcmc/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
index 6edffa4a6dc..3ed9e4f79da 100644
--- a/sci-biology/bedtools/metadata.xml
+++ b/sci-biology/bedtools/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<herd>proxy-maintainers</herd>
diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml
index 45107864e21..0630beec216 100644
--- a/sci-biology/bfast/metadata.xml
+++ b/sci-biology/bfast/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml
index 173e3b48f53..03c4728af26 100644
--- a/sci-biology/biogrep/metadata.xml
+++ b/sci-biology/biogrep/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/biojava/metadata.xml b/sci-biology/biojava/metadata.xml
index 0a18364544e..7f43ec214cc 100644
--- a/sci-biology/biojava/metadata.xml
+++ b/sci-biology/biojava/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<herd>java</herd>
diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml
index 642468c809b..36edac8bc95 100644
--- a/sci-biology/bioperl-db/metadata.xml
+++ b/sci-biology/bioperl-db/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml
index 045af7cc614..2f001d5643e 100644
--- a/sci-biology/bioperl-network/metadata.xml
+++ b/sci-biology/bioperl-network/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml
index f8c7078a281..568fccee860 100644
--- a/sci-biology/bioperl-run/metadata.xml
+++ b/sci-biology/bioperl-run/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
index 210ba364d45..8ee69a9ceae 100644
--- a/sci-biology/bioperl/metadata.xml
+++ b/sci-biology/bioperl/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/biopython/metadata.xml
+++ b/sci-biology/biopython/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml
index d4648212cba..888b33ed05c 100644
--- a/sci-biology/bioruby/metadata.xml
+++ b/sci-biology/bioruby/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/biosql/metadata.xml
+++ b/sci-biology/biosql/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/blat/metadata.xml
+++ b/sci-biology/blat/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/blossoc/metadata.xml
+++ b/sci-biology/blossoc/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml
index e493417070f..6b293c04605 100644
--- a/sci-biology/bowtie/metadata.xml
+++ b/sci-biology/bowtie/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml
index 97a33fbf5c4..b9b42f9174a 100644
--- a/sci-biology/bwa/metadata.xml
+++ b/sci-biology/bwa/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
index bd5607ab16b..0f09fa4c33a 100644
--- a/sci-biology/cd-hit/metadata.xml
+++ b/sci-biology/cd-hit/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/clustal-omega/metadata.xml
+++ b/sci-biology/clustal-omega/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
index 905eba1a07b..541a143720f 100644
--- a/sci-biology/clustalw-mpi/metadata.xml
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/clustalw/metadata.xml
+++ b/sci-biology/clustalw/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/clustalx/metadata.xml
+++ b/sci-biology/clustalx/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/consed/metadata.xml
+++ b/sci-biology/consed/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/cufflinks/metadata.xml
+++ b/sci-biology/cufflinks/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
index 46163bc2a80..9c30532281a 100644
--- a/sci-biology/cutg/cutg-160-r1.ebuild
+++ b/sci-biology/cutg/cutg-160-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=5
DESCRIPTION="Codon usage tables calculated from GenBank"
HOMEPAGE="http://www.kazusa.or.jp/codon/"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
SLOT="0"
LICENSE="public-domain"
diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
index 59b110912ca..0bb97ff1bb0 100644
--- a/sci-biology/cutg/metadata.xml
+++ b/sci-biology/cutg/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/dialign-tx/metadata.xml
+++ b/sci-biology/dialign-tx/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml
index 7bc6ee8ea83..c96cc8f6b0f 100644
--- a/sci-biology/dialign2/metadata.xml
+++ b/sci-biology/dialign2/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer>
<email>jlec@gentoo.org</email>
diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml
index d6b9de8b20a..ecde0dac7cd 100644
--- a/sci-biology/diya/metadata.xml
+++ b/sci-biology/diya/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml
index 469879ba8f5..274bbbb8658 100644
--- a/sci-biology/elph/metadata.xml
+++ b/sci-biology/elph/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-cbstools/metadata.xml
+++ b/sci-biology/embassy-cbstools/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-clustalomega/metadata.xml
+++ b/sci-biology/embassy-clustalomega/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-domainatrix/metadata.xml
+++ b/sci-biology/embassy-domainatrix/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-domalign/metadata.xml
+++ b/sci-biology/embassy-domalign/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-domsearch/metadata.xml
+++ b/sci-biology/embassy-domsearch/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-emnu/metadata.xml
+++ b/sci-biology/embassy-emnu/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-esim4/metadata.xml
+++ b/sci-biology/embassy-esim4/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-hmmer/metadata.xml
+++ b/sci-biology/embassy-hmmer/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-iprscan/metadata.xml
+++ b/sci-biology/embassy-iprscan/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-meme/metadata.xml
+++ b/sci-biology/embassy-meme/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-memenew/metadata.xml b/sci-biology/embassy-memenew/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-memenew/metadata.xml
+++ b/sci-biology/embassy-memenew/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-mira/metadata.xml b/sci-biology/embassy-mira/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-mira/metadata.xml
+++ b/sci-biology/embassy-mira/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-mse/metadata.xml
+++ b/sci-biology/embassy-mse/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-phylipnew/metadata.xml
+++ b/sci-biology/embassy-phylipnew/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-signature/metadata.xml
+++ b/sci-biology/embassy-signature/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-structure/metadata.xml
+++ b/sci-biology/embassy-structure/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-topo/metadata.xml
+++ b/sci-biology/embassy-topo/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy-vienna/metadata.xml
+++ b/sci-biology/embassy-vienna/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/embassy/metadata.xml
+++ b/sci-biology/embassy/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
index 3af936dc156..00f586eeda1 100644
--- a/sci-biology/emboss/metadata.xml
+++ b/sci-biology/emboss/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/eugene/metadata.xml
+++ b/sci-biology/eugene/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml
index 711d805d77e..ff9dbd7b15d 100644
--- a/sci-biology/exonerate/metadata.xml
+++ b/sci-biology/exonerate/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/express/metadata.xml
+++ b/sci-biology/express/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
index b98c9919d24..edc83bb65f9 100644
--- a/sci-biology/fasta/metadata.xml
+++ b/sci-biology/fasta/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml
index 5ee1f51e55d..97f55457dae 100644
--- a/sci-biology/fasttree/metadata.xml
+++ b/sci-biology/fasttree/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml
index e487463fc00..09e954e4895 100644
--- a/sci-biology/finchtv/metadata.xml
+++ b/sci-biology/finchtv/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/flower/metadata.xml b/sci-biology/flower/metadata.xml
index dcaae2095b0..1b21b5edd6d 100644
--- a/sci-biology/flower/metadata.xml
+++ b/sci-biology/flower/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>haskell</herd>
<maintainer>
diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml
index 63d767b84f6..f5376ab7c36 100644
--- a/sci-biology/foldingathome/metadata.xml
+++ b/sci-biology/foldingathome/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/gatk/metadata.xml
+++ b/sci-biology/gatk/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml
index c31e2db7021..4af848231d6 100644
--- a/sci-biology/gibbs/metadata.xml
+++ b/sci-biology/gibbs/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/glimmer/metadata.xml
+++ b/sci-biology/glimmer/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/glimmerhmm/metadata.xml
+++ b/sci-biology/glimmerhmm/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml
index 7d62e2f44e0..1ca1c474ce0 100644
--- a/sci-biology/gmap/metadata.xml
+++ b/sci-biology/gmap/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/goby-cpp/metadata.xml b/sci-biology/goby-cpp/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/goby-cpp/metadata.xml
+++ b/sci-biology/goby-cpp/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml
index 3bc02ac6b32..34b5ca85dc0 100644
--- a/sci-biology/goby/metadata.xml
+++ b/sci-biology/goby/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
index 66fa7662661..a216003f3d9 100644
--- a/sci-biology/hmmer/metadata.xml
+++ b/sci-biology/hmmer/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/iedera/metadata.xml
+++ b/sci-biology/iedera/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/infernal/metadata.xml
+++ b/sci-biology/infernal/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/iqpnni/metadata.xml
+++ b/sci-biology/iqpnni/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/kalign/metadata.xml
+++ b/sci-biology/kalign/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/lagan/metadata.xml
+++ b/sci-biology/lagan/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/last/metadata.xml
+++ b/sci-biology/last/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/mafft/metadata.xml
+++ b/sci-biology/mafft/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/mammoth/metadata.xml b/sci-biology/mammoth/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/mammoth/metadata.xml
+++ b/sci-biology/mammoth/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml
index 79ebcc09421..631ae377637 100644
--- a/sci-biology/maq/metadata.xml
+++ b/sci-biology/maq/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml
index 79ebcc09421..631ae377637 100644
--- a/sci-biology/maqview/metadata.xml
+++ b/sci-biology/maqview/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/mauve/metadata.xml b/sci-biology/mauve/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/mauve/metadata.xml
+++ b/sci-biology/mauve/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/mauvealigner/metadata.xml b/sci-biology/mauvealigner/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/mauvealigner/metadata.xml
+++ b/sci-biology/mauvealigner/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml
index aa6527e1e83..0a1130a3c53 100644
--- a/sci-biology/mcl/metadata.xml
+++ b/sci-biology/mcl/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/meme/metadata.xml
+++ b/sci-biology/meme/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml
index 7a808874b6e..14ccb885116 100644
--- a/sci-biology/metadata.xml
+++ b/sci-biology/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE catmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<catmetadata>
<longdescription lang="en">
The sci-biology category contains software that can be used
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
index a2c7c1a0a6a..db0cf39d223 100644
--- a/sci-biology/mira/metadata.xml
+++ b/sci-biology/mira/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
index 4dfd5b0bdaf..e33216655e6 100644
--- a/sci-biology/mosaik/metadata.xml
+++ b/sci-biology/mosaik/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/mothur/metadata.xml
+++ b/sci-biology/mothur/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
index 8a6a5b986dc..f5495320b9a 100644
--- a/sci-biology/mrbayes/metadata.xml
+++ b/sci-biology/mrbayes/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml
index f82b462e1f9..979e3814da9 100644
--- a/sci-biology/mummer/metadata.xml
+++ b/sci-biology/mummer/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/muscle/metadata.xml
+++ b/sci-biology/muscle/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/ncbi-tools/metadata.xml
+++ b/sci-biology/ncbi-tools/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/newick-utils/metadata.xml
+++ b/sci-biology/newick-utils/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml
index 31592430880..e0cfc5842d3 100644
--- a/sci-biology/njplot/metadata.xml
+++ b/sci-biology/njplot/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/pals/metadata.xml
+++ b/sci-biology/pals/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/paml/metadata.xml
+++ b/sci-biology/paml/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/phrap/metadata.xml
+++ b/sci-biology/phrap/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/phred/metadata.xml
+++ b/sci-biology/phred/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/phylip/metadata.xml
+++ b/sci-biology/phylip/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml
index d0355f85e40..95bf48c3c8f 100644
--- a/sci-biology/phyml/metadata.xml
+++ b/sci-biology/phyml/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription lang="en">
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
index 265affea91d..a0a308bde78 100644
--- a/sci-biology/picard/metadata.xml
+++ b/sci-biology/picard/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild
index 16e71f41f2b..262e4873f3a 100644
--- a/sci-biology/picard/picard-1.103.ebuild
+++ b/sci-biology/picard/picard-1.103.ebuild
@@ -11,7 +11,7 @@ inherit java-pkg-2 java-ant-2
DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
HOMEPAGE="http://picard.sourceforge.net/"
-SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
+SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
LICENSE="Apache-2.0"
SLOT="0"
diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/piler/metadata.xml
+++ b/sci-biology/piler/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/pilercr/metadata.xml
+++ b/sci-biology/pilercr/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
index 80af0e1d036..3c82b56f885 100644
--- a/sci-biology/plink/metadata.xml
+++ b/sci-biology/plink/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml
index 65027f64ec2..1ab8f747304 100644
--- a/sci-biology/poa/metadata.xml
+++ b/sci-biology/poa/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml
index 2cd3c04eeca..11369741f7f 100644
--- a/sci-biology/prank/metadata.xml
+++ b/sci-biology/prank/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml
index 1fbadfaf3b7..fc4a35358af 100644
--- a/sci-biology/primer3/metadata.xml
+++ b/sci-biology/primer3/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml
index 7d2927f1d2f..fe83d786f65 100644
--- a/sci-biology/prints/metadata.xml
+++ b/sci-biology/prints/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/probcons/metadata.xml
+++ b/sci-biology/probcons/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml
index 6e8b2ee66e6..8d831d29bb1 100644
--- a/sci-biology/prodigal/metadata.xml
+++ b/sci-biology/prodigal/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/profphd/metadata.xml
+++ b/sci-biology/profphd/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml
index 075d4b7bcf1..5974edbdaed 100644
--- a/sci-biology/prosite/metadata.xml
+++ b/sci-biology/prosite/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
index 655b161c218..ff46cda4db2 100644
--- a/sci-biology/psipred/metadata.xml
+++ b/sci-biology/psipred/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<maintainer>
diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
index 49afc3c3d53..7e41c1e4c5d 100644
--- a/sci-biology/pysam/metadata.xml
+++ b/sci-biology/pysam/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml
index d4648212cba..888b33ed05c 100644
--- a/sci-biology/qrna/metadata.xml
+++ b/sci-biology/qrna/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/raxml/metadata.xml
+++ b/sci-biology/raxml/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/readseq/metadata.xml b/sci-biology/readseq/metadata.xml
index b198f044f3f..245af9a45b5 100644
--- a/sci-biology/readseq/metadata.xml
+++ b/sci-biology/readseq/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/readseq/readseq-20080420-r1.ebuild b/sci-biology/readseq/readseq-20080420-r1.ebuild
index 43c538beb59..c483fc24202 100644
--- a/sci-biology/readseq/readseq-20080420-r1.ebuild
+++ b/sci-biology/readseq/readseq-20080420-r1.ebuild
@@ -12,7 +12,7 @@ HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
# Originally unversioned at
# http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-source.zip.
# Renamed to the date of the modification and mirrored
-SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
+SRC_URI="https://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
LICENSE="public-domain"
SLOT="0"
diff --git a/sci-biology/readseq/readseq-20100513.ebuild b/sci-biology/readseq/readseq-20100513.ebuild
index 6539ebd427c..3f18380ad04 100644
--- a/sci-biology/readseq/readseq-20100513.ebuild
+++ b/sci-biology/readseq/readseq-20100513.ebuild
@@ -8,7 +8,7 @@ inherit java-pkg-2 java-ant-2
DESCRIPTION="Reads and writes nucleic/protein sequences in various formats"
HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
-SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.zip"
+SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.zip"
LICENSE="public-domain"
SLOT="0"
diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml
index 734fcff7e21..dd0f62c9e61 100644
--- a/sci-biology/rebase/metadata.xml
+++ b/sci-biology/rebase/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/rebase/rebase-1507.ebuild b/sci-biology/rebase/rebase-1507.ebuild
index 6b32ba231a2..0088b50aa25 100644
--- a/sci-biology/rebase/rebase-1507.ebuild
+++ b/sci-biology/rebase/rebase-1507.ebuild
@@ -8,7 +8,7 @@ MY_PV=${PV#1}
DESCRIPTION="A restriction enzyme database"
HOMEPAGE="http://rebase.neb.com"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
SLOT="0"
LICENSE="public-domain"
diff --git a/sci-biology/rebase/rebase-1508.ebuild b/sci-biology/rebase/rebase-1508.ebuild
index f171a569ee8..1bfa8ba6880 100644
--- a/sci-biology/rebase/rebase-1508.ebuild
+++ b/sci-biology/rebase/rebase-1508.ebuild
@@ -8,7 +8,7 @@ MY_PV=${PV#1}
DESCRIPTION="A restriction enzyme database"
HOMEPAGE="http://rebase.neb.com"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
SLOT="0"
LICENSE="public-domain"
diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/recon/metadata.xml
+++ b/sci-biology/recon/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/repeatmasker-libraries/metadata.xml
+++ b/sci-biology/repeatmasker-libraries/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/repeatmasker/metadata.xml
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/rmblast/metadata.xml
+++ b/sci-biology/rmblast/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml
index b243b0c8da6..796cc13fdf5 100644
--- a/sci-biology/rnaview/metadata.xml
+++ b/sci-biology/rnaview/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml
index 74dc02bc982..719203ab7c3 100644
--- a/sci-biology/samtools/metadata.xml
+++ b/sci-biology/samtools/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml
index 33794f43ab0..096ea3fa581 100644
--- a/sci-biology/seaview/metadata.xml
+++ b/sci-biology/seaview/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/seqan/metadata.xml
+++ b/sci-biology/seqan/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/shrimp/metadata.xml
+++ b/sci-biology/shrimp/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml
index cfcd5be131d..35b54f0486f 100644
--- a/sci-biology/sibsim4/metadata.xml
+++ b/sci-biology/sibsim4/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml
index ea973127900..9d374020460 100644
--- a/sci-biology/sim4/metadata.xml
+++ b/sci-biology/sim4/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/snpfile/metadata.xml
+++ b/sci-biology/snpfile/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/stride/metadata.xml
+++ b/sci-biology/stride/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild
index 0848427631a..ea01b1fa76b 100644
--- a/sci-biology/stride/stride-20011129-r1.ebuild
+++ b/sci-biology/stride/stride-20011129-r1.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Protein secondary structure assignment from atomic coordinates"
HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/"
SRC_URI="
ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz
- http://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2"
+ https://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2"
SLOT="0"
LICENSE="STRIDE"
diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml
index 9a577185ee3..b24ed27a414 100644
--- a/sci-biology/t-coffee/metadata.xml
+++ b/sci-biology/t-coffee/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
index 36cf4a13894..a4b99d4d752 100644
--- a/sci-biology/tophat/metadata.xml
+++ b/sci-biology/tophat/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/transfac/metadata.xml b/sci-biology/transfac/metadata.xml
index d07df4fd4db..96faf337489 100644
--- a/sci-biology/transfac/metadata.xml
+++ b/sci-biology/transfac/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml
index cbdeede346f..1e490902a62 100644
--- a/sci-biology/tree-puzzle/metadata.xml
+++ b/sci-biology/tree-puzzle/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml
index e351ff6c1fa..f315d73937a 100644
--- a/sci-biology/treeviewx/metadata.xml
+++ b/sci-biology/treeviewx/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/trf/metadata.xml
+++ b/sci-biology/trf/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml
index 55de1683677..83f4b1ae09f 100644
--- a/sci-biology/trnascan-se/metadata.xml
+++ b/sci-biology/trnascan-se/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml
index a3c0f91c8a0..7c1030d54a9 100644
--- a/sci-biology/uchime/metadata.xml
+++ b/sci-biology/uchime/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
index f1f3ccfb77e..2abe32d164a 100644
--- a/sci-biology/ucsc-genome-browser/metadata.xml
+++ b/sci-biology/ucsc-genome-browser/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>
diff --git a/sci-biology/unafold/metadata.xml b/sci-biology/unafold/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/unafold/metadata.xml
+++ b/sci-biology/unafold/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/update-blastdb/metadata.xml
+++ b/sci-biology/update-blastdb/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/vaal/metadata.xml
+++ b/sci-biology/vaal/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
index c45e9f4dea0..7c77cff5bca 100644
--- a/sci-biology/vcftools/metadata.xml
+++ b/sci-biology/vcftools/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/velvet/metadata.xml
+++ b/sci-biology/velvet/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
index 50f4e02d4a1..e4155f10561 100644
--- a/sci-biology/vienna-rna/metadata.xml
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<longdescription>
diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml
index 8e4a7436807..c651ff9580c 100644
--- a/sci-biology/wgs-assembler/metadata.xml
+++ b/sci-biology/wgs-assembler/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<upstream>
diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml
index f17a827e310..fdb6c59d50a 100644
--- a/sci-biology/wise/metadata.xml
+++ b/sci-biology/wise/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml
index e4a717e691b..3756a4d4e2f 100644
--- a/sci-biology/yass/metadata.xml
+++ b/sci-biology/yass/metadata.xml
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci-biology</herd>
<use>