[med-svn] [Git][med-team/barrnap][master] 5 commits: d/patches/use_both_hmmsets: not needed since before 0.7+dfsg-1
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Sep 16 17:00:01 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / barrnap
Commits:
8abbc9c1 by Michael R. Crusoe at 2023-09-16T13:37:19+02:00
d/patches/use_both_hmmsets: not needed since before 0.7+dfsg-1
- - - - -
2b385449 by Michael R. Crusoe at 2023-09-16T13:38:14+02:00
d/tests/control: hmmer is now available on arm64/armhf; test there as well.
- - - - -
13bf15d1 by Michael R. Crusoe at 2023-09-16T17:20:05+02:00
refresh the databases using the latest SILVA database which is DFSG compliant (CC-BY-4.0).
- - - - -
5306d2f4 by Michael R. Crusoe at 2023-09-16T17:21:57+02:00
d/patches/use_debian_dirs: document author, no need to forward upstream
- - - - -
8d29fbae by Michael R. Crusoe at 2023-09-16T17:21:57+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/copyright
- debian/patches/series
- + debian/patches/update_dbs
- − debian/patches/use_both_hmmsets
- debian/patches/use_debian_dirs
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+barrnap (0.9+dfsg-4) unstable; urgency=medium
+
+ * Team upload.
+ * d/patches/use_both_hmmsets: not needed since before 0.7+dfsg-1
+ * d/tests/control: hmmer is now available on arm64/armhf; test there
+ as well.
+ * d/patches/update_dbs: refresh the databases using the latest SILVA
+ database which is DFSG compliant (CC-BY-4.0).
+ * d/copyright: document the provenance and licensing for
+ d/patches/update_dbs; update homepage URL
+ * d/patches/use_debian_dirs: document author, no need to forward upstream
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 16 Sep 2023 16:36:40 +0200
+
barrnap (0.9+dfsg-3) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -1,32 +1,18 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: barrnap
-Source: https://github.com/Victorian-Bioinformatics-Consortium/barrnap
-Files-Excluded: binaries/* build/* LICENSE.SILVA
+Source: https://github.com/tseemann/barrnap
+Files-Excluded: binaries/* LICENSE.SILVA
Files: *
Copyright:
Copyright 2013 Torsten Seemann <torsten.seemann at monash.edu>
License: GPL-3+
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
- .
- On Debian systems, the complete text of the GNU General
- Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
Files: db/*
Copyright:
Copyright 2013 Torsten Seemann <torsten.seemann at monash.edu>
-License: CC0
+Comment: the full text of CC0 is available at /usr/share/common-licenses/CC0-1.0
+License: CC0-1.0
The HMMs in the db/ directory have been built from data sources covered by the
following license:
.
@@ -50,3 +36,66 @@ License: CC0
.
When using or citing the work, you should not imply endorsement by the author
or the affirmer.
+
+Files: debian/*
+Copyright: 2014-2020 Sascha Steinbiss <sascha at steinbiss.name>
+License: GPL-3+
+
+Files: debian/patches/update_dbs
+Copyright: 2023 Michael R. Crusoe <crusoe at debian.org>
+License: CC0-1.0 and CC-BY-4.0
+ This patch was created from data in RFAM 15.9 (licensed CC0-1.0)
+ and SILVA 138.1 (licensesd CC-BY-4.0) using the script from
+ https://github.com/tseemann/barrnap/pull/67/files#diff-6bfb761b8f7e87e04787fdc57a57f0a84bba1c774c32c1b6f08bf8ca41129531
+ a.k.a https://github.com/mr-c/barrnap/blob/fd2d147a62c8d5aee45b56c6d56c9310b8383cf6/build/build_HMMs.sh
+ and only software packages from Debian main
+ .
+ RFAM license
+ (https://ftp.ebi.ac.uk/pub/databases/Rfam/14.9/COPYING)
+ ===
+ Rfam version 14.9 was produced at the European Bioinformatics Institute.
+ Rfam is based on a sequence database called Rfamseq. The genome-centric
+ version of Rfam is built from a collection of reference genomes,
+ which are provided by Uniprot proteomes.
+ .
+ Rfam is freely available under the Creative Commons Zero ("CC0")
+ licence. (http://creativecommons.org/publicdomain/zero/1.0/)
+ .
+ Rfam is powered by the Infernal package (http://eddylab.org/infernal/).
+ The current lead developer of Infernal is Eric Nawrocki,
+ at the National Center for Biotechnology Information (NCBI,
+ nawrocke at ncbi.nlm.nih.gov).
+ ===
+ .
+ SILVA version 138+ license
+ (https://www.arb-silva.de/fileadmin/silva_databases/release_138_1/LICENSE.txt)
+ ===
+ As of release 138 the SILVA databases, its taxonomy, and all files provided for
+ download are licensed unter Creative Commons Attribution 4.0 (CC-BY 4.0).
+ .
+ All data is freely available for academic and commercial use as long as SILVA
+ is credited as original author and a link to the full license is provided.
+ .
+ The full license is available:
+ https://creativecommons.org/licenses/by/4.0/ and
+ https://creativecommons.org/licenses/by/4.0/legalcode
+ ===
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
+
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,2 @@
+update_dbs
use_debian_dirs
-use_both_hmmsets
=====================================
debian/patches/update_dbs
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/use_both_hmmsets deleted
=====================================
@@ -1,58 +0,0 @@
-Description: Use_both_hmmsets
---- a/bin/barrnap
-+++ b/bin/barrnap
-@@ -3,6 +3,7 @@
- use warnings;
- use List::Util qw(max);
- use FindBin;
-+use File::Temp qw/ tempfile tempdir /;
- use File::Temp;
-
- # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-@@ -64,6 +65,7 @@
- my $hmmdb = "$DBDIR/$kdom.hmm";
- err("Can't find database: $hmmdb") unless -r $hmmdb;
- msg("Using database: $hmmdb");
-+my $nonfreehmmdb = "$DBDIR/nonfree/$kdom.hmm";
-
- # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # check if user is piping to STDIN
-@@ -84,6 +86,20 @@
- # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # run the external command
-
-+if (-e $nonfreehmmdb) {
-+ # prepare full pHMM file (with nonfree if it exists)
-+ open ( HMMDB, "<", $hmmdb ) or die "Could not open file $hmmdb: $!";
-+ open ( NONFREE, "<", $nonfreehmmdb );
-+ my ($tmpfile, $tmpfilename) = tempfile();
-+ while ( my $line = <HMMDB> ) {
-+ print $tmpfile $line;
-+ }
-+ while ( my $line = <NONFREE> ) {
-+ print $tmpfile $line;
-+ }
-+ $hmmdb = $tmpfilename
-+}
-+
- msg("Scanning $fasta for $kdom rRNA genes... please wait");
- my $opts = "--cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout";
- my $cmd = "nhmmer $opts '$hmmdb' '$fasta'";
-@@ -123,7 +139,7 @@
- # check for incomplete alignments
- my $note = '';
- my $len = $end-$begin+1;
--
-+
- if ( $len < int($reject * $LENG{$gene}) ) {
- msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
- next HIT;
-@@ -144,7 +160,7 @@
- ];
- }
-
--# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-+# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
- # output a sorted GFF3
-
- sub gff_sort {
=====================================
debian/patches/use_debian_dirs
=====================================
@@ -1,4 +1,6 @@
Description: Make sure we use correct paths for Debian policy
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Forwarded: not-needed
--- a/bin/barrnap
+++ b/bin/barrnap
@@ -1,4 +1,4 @@
=====================================
debian/tests/control
=====================================
@@ -2,4 +2,4 @@ Tests: test-example
Depends: @
Restrictions: allow-stderr
# Depends hmmer, which is available on the following architectures
-Architecture: any-amd64 any-i386 powerpc ppc64 x32
+Architecture: any-amd64 any-i386 arm64 armhf powerpc ppc64 x32
View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/compare/e97e818693d21ba70de8f8a2014bff854aa4db9a...8d29fbae3df62b006f4f3c78fb7f3c0088b28af5
--
View it on GitLab: https://salsa.debian.org/med-team/barrnap/-/compare/e97e818693d21ba70de8f8a2014bff854aa4db9a...8d29fbae3df62b006f4f3c78fb7f3c0088b28af5
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230916/fae3a9c6/attachment-0001.htm>
More information about the debian-med-commit
mailing list