[med-svn] [Git][med-team/resfinder][master] 3 commits: Add autopkgtest script as user example
Andreas Tille
gitlab at salsa.debian.org
Fri Nov 15 12:46:22 GMT 2019
Andreas Tille pushed to branch master at Debian Med / resfinder
Commits:
a8742912 by Andreas Tille at 2019-11-15T12:05:04Z
Add autopkgtest script as user example
- - - - -
2f153781 by Andreas Tille at 2019-11-15T12:33:16Z
Upload to new
- - - - -
a7c79f41 by Andreas Tille at 2019-11-15T12:42:56Z
Manpage
- - - - -
9 changed files:
- + debian/README.test
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/manpages
- debian/resfinder-example.install
- + debian/resfinder.docs
- + debian/resfinder.py.1
- debian/rules
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by installing the package resfinder-example and
+running the provided test which can be found afterwards in the current dir:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-resfinder (3.2-1) UNRELEASED; urgency=medium
+resfinder (3.2-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #944789)
- -- Andreas Tille <tille at debian.org> Thu, 07 Nov 2019 12:41:11 +0100
+ -- Andreas Tille <tille at debian.org> Fri, 15 Nov 2019 13:33:04 +0100
=====================================
debian/control
=====================================
@@ -19,7 +19,7 @@ Depends: ${python3:Depends},
python3-cgecore,
python3-tabulate,
ncbi-blast+-legacy
-Description: identifies acquired antimicrobial resistance genes
+Description: identify acquired antimicrobial resistance genes
ResFinder identifies acquired antimicrobial resistance genes in total or
partial sequenced isolates of bacteria.
.
@@ -34,7 +34,7 @@ Package: resfinder-example
Architecture: all
Depends: ${misc:Depends},
Recommends: resfinder
-Description: identifies acquired antimicrobial resistance genes (example data)
+Description: identify acquired antimicrobial resistance genes (example data)
ResFinder identifies acquired antimicrobial resistance genes in total or
partial sequenced isolates of bacteria.
.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=resfinder.py
+help2man --no-info --no-discard-stderr \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/resfinder-example.install
=====================================
@@ -1 +1,2 @@
-test.fsa usr/share/doc/resfinder/examples
+test.fsa usr/share/doc/resfinder/examples
+debian/tests/run-unit-test usr/share/doc/resfinder
=====================================
debian/resfinder.docs
=====================================
@@ -0,0 +1 @@
+debian/README.test
=====================================
debian/resfinder.py.1
=====================================
@@ -0,0 +1,60 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.11.
+.TH RESFINDER.PY "1" "November 2019" "resfinder.py 3.2" "User Commands"
+.SH NAME
+resfinder.py \- identify acquired antimicrobial resistance genes
+.SH SYNOPSIS
+.B resfinder.py
+[\-h] \fB\-i\fR INPUTFILE [INPUTFILE ...] [\-o OUT_PATH]
+[\-tmp TMP_DIR] [\-mp METHOD_PATH] [\-p DB_PATH]
+[\-d DATABASES] [\-l MIN_COV] [\-t THRESHOLD]
+[\-ao ACQ_OVERLAP] [\-matrix] [\-x] [\-q]
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR INPUTFILE [INPUTFILE ...], \fB\-\-inputfile\fR INPUTFILE [INPUTFILE ...]
+FASTA or FASTQ input files.
+.TP
+\fB\-o\fR OUT_PATH, \fB\-\-outputPath\fR OUT_PATH
+Path to blast output
+.TP
+\fB\-tmp\fR TMP_DIR, \fB\-\-tmp_dir\fR TMP_DIR
+Temporary directory for storage of the results from
+the external software.
+.TP
+\fB\-mp\fR METHOD_PATH, \fB\-\-methodPath\fR METHOD_PATH
+Path to method to use (kma or blastn)
+.TP
+\fB\-p\fR DB_PATH, \fB\-\-databasePath\fR DB_PATH
+Path to the databases
+.TP
+\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES
+Databases chosen to search in \- if none are specified
+all are used
+.TP
+\fB\-l\fR MIN_COV, \fB\-\-min_cov\fR MIN_COV
+Minimum coverage
+.TP
+\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
+Blast threshold for identity
+.TP
+\fB\-ao\fR ACQ_OVERLAP, \fB\-\-acq_overlap\fR ACQ_OVERLAP
+Genes are allowed to overlap this number of
+nucleotides. Default: 30.
+.TP
+\fB\-matrix\fR, \fB\-\-matrix\fR
+Gives the counts all all called bases at each position
+in each mapped template. Columns are: reference base,
+A count, C count, G count, T count, N count, \- count.
+.TP
+\fB\-x\fR, \fB\-\-extented_output\fR
+Give extented output with allignment files, template
+and query hits in fasta and a tab seperated file with
+gene profile results
+.HP
+\fB\-q\fR, \fB\-\-quiet\fR
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/rules
=====================================
@@ -2,3 +2,6 @@
%:
dh $@ --with python3
+
+override_dh_installman:
+ dh_installman --language=C
View it on GitLab: https://salsa.debian.org/med-team/resfinder/compare/8f57c4646a7b3e59ec16a02f062430cec365a5e1...a7c79f41623e439563c1238fdb2252b75cc85a83
--
View it on GitLab: https://salsa.debian.org/med-team/resfinder/compare/8f57c4646a7b3e59ec16a02f062430cec365a5e1...a7c79f41623e439563c1238fdb2252b75cc85a83
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