Pranav Ballaney pushed to branch master at Debian Med / norsp
Commits: 750fd707 by Pranav Ballaney at 2020-06-04T06:50:48+05:30 Add missing dependency - - - - - 0280ca03 by Pranav Ballaney at 2020-06-04T06:50:58+05:30 Add manpage - - - - - 8a3ac71a by Pranav Ballaney at 2020-06-04T07:01:14+05:30 Improve manpage - - - - - 7378c214 by Pranav Ballaney at 2020-06-04T07:04:08+05:30 Add autopkgtests - - - - - fd64e3a3 by Pranav Ballaney at 2020-06-04T07:04:52+05:30 Install docs - - - - - 10 changed files: - + debian/README.test - debian/changelog - debian/control - + debian/createmanpages - + debian/docs - + debian/examples - + debian/manpages - + debian/norsp.1 - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +norsp (1.0.6-5) UNRELEASED; urgency=medium + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Pranav Ballaney ] + * Add missing dependency + * Add manpage + * Add autopkgtests + * Install docs + + -- Pranav Ballaney <[email protected]> Thu, 04 Jun 2020 07:04:12 +0530 + norsp (1.0.6-4) unstable; urgency=medium * pp-popularity-contest only suggested ===================================== debian/control ===================================== @@ -14,12 +14,12 @@ Homepage: https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_S Package: norsp Architecture: all Depends: ${misc:Depends}, - ${perl:Depends} + ${perl:Depends}, + pp-popularity-contest Recommends: blast2, librg-utils-perl, profphd, ncoils -Suggests: pp-popularity-contest Description: predictor of non-regular secondary structure NORSp is a publicly available predictor for disordered regions in proteins. Specifically, it predicts long regions with no regular secondary structure. ===================================== 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 $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=${PROGNAME} +help2man --no-info --no-discard-stderr --help-option="multinom --help" \ + --name="$NAME" \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +echo "$MANDIR/*.1" > debian/manpages + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT ===================================== debian/docs ===================================== @@ -0,0 +1,2 @@ +debian/tests/run-unit-test +debian/README.test \ No newline at end of file ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +examples/* \ No newline at end of file ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/norsp.1 ===================================== @@ -0,0 +1,28 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13. +.TH NORSP "1" "June 2020" "norsp 1.0.6" "User Commands" +.SH NAME +norsp \- predictor of non-regular secondary structure +.SH SYNOPSIS +.B norsp +[\fI\,options\/\fR] \fB\-fileSeq\fR seq_file \fB\-fileHssp\fR hssp_file\/ \fB\-filePhd\fR phd_file +.HP +\fB\-filePhdHtm\fR phdHtm_file \fB\-fileCoils\fR coils_file \fB\-o\fR output_file +.SH DESCRIPTION +.TP +Options: +.HP +\fB\-help\fR print this help +.HP +\fB\-html\fR print HTML output(default=0) +.HP +\fB\-win\fR window size(default=70) +.HP +\fB\-secCut\fR max structure content(default=12) +.HP +\fB\-accLen\fR minimum consecutive exposed residues(default=10) +.HP +\fB\-\-(no)debug\fR print debug info(default=nodebug) +.HP +.SH AUTHOR + This manpage was written by Pranav Ballaney for the Debian distribution and + can be used for any other usage of the program. ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,22 @@ +#!/bin/bash +set -e + +pkg=norsp + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +gunzip -r * +#do_stuff_to_test_package# +norsp -fileSeq query.fasta -fileHssp query.hssp -filePhd query.prof -filePhdHtm query.phdHtm -fileCoils query.coils -o output +head output \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/norsp/-/compare/b511188f7bab8ba423fce83f87c4c68b677a9fc3...fd64e3a3e87efb082964a02d63c6bfa6f1b02a10 -- View it on GitLab: https://salsa.debian.org/med-team/norsp/-/compare/b511188f7bab8ba423fce83f87c4c68b677a9fc3...fd64e3a3e87efb082964a02d63c6bfa6f1b02a10 You're receiving this email because of your account on salsa.debian.org.
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