[med-svn] [Git][med-team/norsp][master] 5 commits: Add missing dependency
Pranav Ballaney
gitlab at salsa.debian.org
Thu Jun 4 02:35:26 BST 2020
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 <ballaneypranav at gmail.com> 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
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