[med-svn] [Git][med-team/resfinder][master] 4 commits: Initial packaging
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 25 14:48:50 BST 2018
Andreas Tille pushed to branch master at Debian Med / resfinder
Commits:
0a51edaf by Andreas Tille at 2018-06-25T13:46:49+02:00
Initial packaging
- - - - -
86815e3e by Andreas Tille at 2018-06-25T13:47:02+02:00
New upstream version 2.3.0
- - - - -
1e627cc7 by Andreas Tille at 2018-06-25T13:47:04+02:00
Update upstream source from tag 'upstream/2.3.0'
Update to upstream version '2.3.0'
with Debian dir dbaa902f3189d217c9081c4026fc306000983858
- - - - -
d8a48b9a by Andreas Tille at 2018-06-25T15:48:29+02:00
Several fixes
- - - - -
11 changed files:
- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/install
- + debian/lintian-overrides
- + debian/rules
- + debian/source/format
- + debian/upstream/metadata
- + debian/watch
- resfinder.pl
Changes:
=====================================
debian/changelog
=====================================
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+resfinder (2.3.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 07 Jun 2018 21:55:00 +0200
=====================================
debian/compat
=====================================
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+11
=====================================
debian/control
=====================================
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,28 @@
+Source: resfinder
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/resfinder
+Vcs-Git: https://salsa.debian.org/med-team/resfinder.git
+Homepage: https://bitbucket.org/genomicepidemiology/resfinder
+
+Package: resfinder
+Architecture: any
+Depends: ${perl:Depends},
+ ${python:Depends},
+ ${misc:Depends},
+ bioperl,
+ ncbi-blast+-legacy
+Description: identifies acquired antimicrobial resistance genes
+ ResFinder identifies acquired antimicrobial resistance genes in total or
+ partial sequenced isolates of bacteria.
+ .
+ ResFinder that uses BLAST for identification of acquired antimicrobial
+ resistance genes in whole-genome data. As input, the method can use both
+ pre-assembled, complete or partial genomes, and short sequence reads
+ from four different sequencing platforms. The method was evaluated on
+ 1862 GenBank files containing 1411 different resistance genes, as well
+ as on 23 de-novo-sequenced isolates.
=====================================
debian/copyright
=====================================
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,24 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: resfinder
+Source: https://bitbucket.org/genomicepidemiology/resfinder.git
+
+Files: *
+Copyright: 2012-2018 Ole Lund, Technical University of Denmark
+License: Apache-2.0
+
+Files: debian/*
+Copyright: 2018 Andreas Tille <tille at debian.org>
+License: Apache-2.0
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems you can find the full text of the Apache-2.0
+ license at /usr/share/common-licenses/Apache-2.0.
=====================================
debian/install
=====================================
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+*_DB /usr/bin
+*.pl /usr/bin
=====================================
debian/lintian-overrides
=====================================
--- /dev/null
+++ b/debian/lintian-overrides
@@ -0,0 +1,4 @@
+# see discussion on Debian Med mailing list
+# https://lists.debian.org/debian-med/2018/06/msg00042.html
+# and following mails in thread
+resfinder: script-with-language-extension usr/bin/resfinder.pl
=====================================
debian/rules
=====================================
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+%:
+ dh $@
+
+override_dh_auto_build:
+override_dh_auto_install:
+ echo "Upstream install target just fetches BioPerl which is now installed via Depends"
=====================================
debian/source/format
=====================================
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/upstream/metadata
=====================================
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Ea Zankari and Henrik Hasman and Salvatore Cosentino and Martin Vestergaard and Simon Rasmussen and Ole Lund and Frank M. Aarestrup and Mette Voldby Larsen
+ Title: Identification of acquired antimicrobial resistance genes
+ Journal: Journal of Antimicrobial Chemotherapy
+ Year: 2012
+ Volume: 67
+ Number: 11
+ Pages: 2640-4
+ DOI: 10.1093/jac/dks261
+ PMID: 22782487
+ URL: https://academic.oup.com/jac/article/67/11/2640/707208
+ eprint: https://academic.oup.com/jac/article-pdf/67/11/2640/2085909/dks261.pdf
=====================================
debian/watch
=====================================
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,9 @@
+version=4
+
+https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=tags .*/@ANY_VERSION@@ARCHIVE_EXT@
+
+#opts="mode=git,pretty=2.1+git%cd.%h" \
+# https://bitbucket.org/genomicepidemiology/resfinder.git HEAD
+
+# In branches is totally different code ov not yet released Python code version 4.x
+# https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=branches .*/@ANY_VERSION@@ARCHIVE_EXT@
=====================================
resfinder.pl
=====================================
--- a/resfinder.pl
+++ b/resfinder.pl
@@ -10,7 +10,7 @@ use Try::Tiny::Retry;
use constant PROGRAM_NAME => 'ResFinder_v2.pl';
use constant PROGRAM_NAME_LONG => 'Findes antimicrobial resitance genes for a sequence or genome';
-use constant VERSION => '2.1';
+use constant VERSION => '2.3';
#Global variables
my $BLAST;
@@ -465,7 +465,7 @@ foreach my $element(@Antimicrobial){
my $Seqs_genome_ref = grep_ids(-seqs => $Seqs_input, -ids => \@array_for_getting_genome_seq);
for (@{ $Seqs_genome_ref }) {
my $contig = lc($_->seq);
- my $length_contig = length($contig); #Redundant, da jeg ogsΠv.h.a. bioperl finder hit length
+ my $length_contig = length($contig); #Redundant, da jeg ogs� v.h.a. bioperl finder hit length
# Getting the right sub_contig depends on which strand the hit is on
# If the hit is on the +1
@@ -490,7 +490,7 @@ foreach my $element(@Antimicrobial){
$variant = 4;
$major_variants_detector = 1;
$sub_contig = substr($contig, 0, ( $HIT_START{$data} + (($QUERY_LENGTH{$data} + $no_gaps_gene) - $QUERY_START{$data})));
- #If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||Ê|||Ê||") should be preceeded by spaces
+ #If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||�|||�||") should be preceeded by spaces
$spaces_hit = $QUERY_START{$data} - $HIT_START{$data} + 1;
$spaces_match_string = $QUERY_START{$data};
} else {
@@ -705,7 +705,7 @@ foreach my $element(@Antimicrobial){
$variant = 4;
$major_variants_detector = 1;
$sub_contig = substr($contig, 0, ( $HIT_START{$data} + (($QUERY_LENGTH{$data} + $no_gaps_gene) - $QUERY_START{$data})));
- # If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||Ê|||Ê||") should be preceeded by spaces
+ # If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||�|||�||") should be preceeded by spaces
$spaces_hit = $QUERY_START{$data} - $HIT_START{$data} + 1;
$spaces_match_string = $QUERY_START{$data};
}
@@ -860,7 +860,7 @@ foreach my $element(@Antimicrobial){
#print $ABres_substr . "\n";
push(@{$GENE_ALIGN_QUERY_HASH{$gene}}, $ABres_substr);
- #Printing spaces before the match string with the "||Ê||||Ê||Ê||" and the string itself
+ #Printing spaces before the match string with the "||�||||�||�||" and the string itself
#print " ";
my $string_spaces = ""; #For saving the spaces as a string of spaces instead of a number of spaces
for (my $i = 1 ; $i < $spaces_match_string; ++$i){
@@ -969,7 +969,7 @@ foreach my $key (sort keys %GENE_RESULTS_HASH2) {
$outStr = $outStr.": WARNING2, ";
}
$alignment .= $outStr."ID: ".@$array[1]."%, HSP/Length: ".@$array[3]."/".@$array[2]. ", Contig name: ".@$array[4].", Position: ".@$array[5]."\n\n";
- $hits_in_seq .= ">".$outStr."ID: ".@$array[1]."%, HSP/Length: ".@$array[3]."/".@$array[2]. ", Positions in reference: ".$qStart."..".$qEnd.", Contig name: ".@$array[4].", Position: ".@$array[5]."\n"; #mŒske forkert text
+ $hits_in_seq .= ">".$outStr."ID: ".@$array[1]."%, HSP/Length: ".@$array[3]."/".@$array[2]. ", Positions in reference: ".$qStart."..".$qEnd.", Contig name: ".@$array[4].", Position: ".@$array[5]."\n"; #m�ske forkert text
$resalign .= ">".@$array[7]."\n";
# now print the alleles
View it on GitLab: https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a
--
View it on GitLab: https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a
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