Nilesh Patra pushed to branch master at Debian Med / surpyvor
Commits: 62f3a35c by Nilesh Patra at 2021-07-13T19:43:22+05:30 Add python3-upsetplot to Depends - - - - - 55e6f42d by Nilesh Patra at 2021-07-13T14:20:12+00:00 Add manpage - - - - - 84af058b by Nilesh Patra at 2021-07-13T19:56:27+05:30 d/control: Minor fix - - - - - 530f6ff6 by Nilesh Patra at 2021-07-13T19:57:10+05:30 Upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - + debian/createmanpages - + debian/manpages - + debian/surpyvor.1 Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,5 @@ -surpyvor (0.5-1) UNRELEASED; urgency=medium +surpyvor (0.5-1) unstable; urgency=medium * Initial release (Closes: #990883) - -- Steffen Moeller <[email protected]> Sat, 10 Jul 2021 00:01:07 +0200 + -- Steffen Moeller <[email protected]> Tue, 13 Jul 2021 19:52:30 +0530 ===================================== debian/control ===================================== @@ -21,13 +21,14 @@ Depends: python3-cyvcf2, python3-matplotlib-venn, survivor, + python3-upsetplot, ${misc:Depends}, ${python3:Depends}, Description: modification of VCF files with SURVIVOR SURVIVOR is a tool set for simulating/evaluating - structural variantions, merging and comparing SVs within + structural variations, merging and comparing SVs within and among samples, and includes various methods to - reformat or summarize structural variantions. + reformat or summarize structural variations. . This package provides a Python wrapper to help with its integration in various Python-based workflows. ===================================== debian/createmanpages ===================================== @@ -0,0 +1,29 @@ +#!/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 $DEBFULLNAME for the Debian distribution and\n \ +can be used for any other usage of the program.\ +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=surpyvor +help2man --no-info --no-discard-stderr --help-option="-h" \ + --name="$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/surpyvor.1 ===================================== @@ -0,0 +1,39 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16. +.TH SURPYVOR "1" "July 2021" "surpyvor 0.5" "User Commands" +.SH NAME +surpyvor \- modification of VCF files with SURVIVOR +.SH DESCRIPTION +usage: surpyvor [\-h] [\-v] {merge,highsens,highconf,prf,venn,upset} ... +.PP +A wrapper around SURVIVOR, with convenience functions. +.SS "optional arguments:" +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-v\fR, \fB\-\-version\fR +Print version and quit. +.SS "[sub-commands]:" +.IP +{merge,highsens,highconf,prf,venn,upset} +.TP +merge +merging vcf files of SVs +.TP +highsens +get union of SV vcfs +.TP +highconf +get intersection of SV vcfs +.TP +prf +calculate precision, recall and F\-measure +.TP +venn +Make venn diagram for 2 or 3 SV vcf files +.TP +upset +Make upset plot for multiple SV vcf files +.SH AUTHOR + This manpage was written by Nilesh Patra for the Debian distribution and + can be used for any other usage of the program. View it on GitLab: https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af -- View it on GitLab: https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af You're receiving this email because of your account on salsa.debian.org.
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