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 <[email protected]> Thu, 07 Nov 2019 12:41:11 +0100 + -- Andreas Tille <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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