Andreas Tille pushed to branch master at Debian Med / umis
Commits: 7c9f49ef by Andreas Tille at 2019-04-13T08:29:56Z Add manpage - - - - - a3306794 by Andreas Tille at 2019-04-13T08:35:41Z Upload to new - - - - - fe00672b by Andreas Tille at 2019-04-13T08:45:18Z Silence lintian about false positive - - - - - 5 changed files: - debian/changelog - + debian/createmanpages - + debian/manpages - + debian/umis-examples.lintian-overrides - + debian/umis.1 Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,5 @@ -umis (1.0.3-1) UNRELEASED; urgency=medium +umis (1.0.3-1) unstable; urgency=medium - * Initial release (Closes: #<bug>) + * Initial release (Closes: #926995) - -- Andreas Tille <[email protected]> Sat, 13 Apr 2019 07:12:50 +0200 + -- Andreas Tille <[email protected]> Sat, 13 Apr 2019 10:35:26 +0200 ===================================== debian/createmanpages ===================================== @@ -0,0 +1,27 @@ +#!/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\nThis manpage was written by $DEBFULLNAME for the Debian distribution and +can be used for any other usage of the program. +" + +# If program name is different from package name or title should be +# different from package short description change this here +progname=${PROGNAME} +help2man --no-info --no-discard-stderr --help-option=" " \ + --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/umis-examples.lintian-overrides ===================================== @@ -0,0 +1,5 @@ +# These files are needed in compressed and uncompressed form +umis-examples: duplicated-compressed-file usr/share/doc/umis/examples/CEL-Seq/SRP036633_1.fastq.gz +umis-examples: duplicated-compressed-file usr/share/doc/umis/examples/CEL-Seq/SRP036633_2.fastq.gz +umis-examples: duplicated-compressed-file usr/share/doc/umis/examples/tagcount/cb-histogram.txt.gz + ===================================== debian/umis.1 ===================================== @@ -0,0 +1,62 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8. +.TH UMIS "1" "April 2019" "umis 1.0.3" "User Commands" +.SH NAME +umis \- tools for processing UMI RNA-tag data +.SH SYNOPSIS +.B umis +[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]... +.SH OPTIONS +.TP +\fB\-\-help\fR +Show this message and exit. +.SS "Commands:" +.TP +add_uid +Adds UID:[samplebc cellbc umi] to readname for... +.TP +bamtag +Convert a BAM/SAM with fastqtransformed read names +to... +.TP +cb_filter +Filters reads with non\-matching barcodes Expects... +.TP +cb_histogram +Counts the number of reads for each cellular barcode... +.TP +demultiplex_cells +Demultiplex a fastqtransformed FASTQ file into a... +.TP +demultiplex_samples +Demultiplex a fastqtransformed FASTQ file into a... +.TP +fastqtransform +Transform input reads to the tagcounts compatible... +.TP +fasttagcount +Count up evidence for tagged molecules, this... +.TP +kallisto +Convert fastqtransformed file to output format... +.TP +mb_filter +Filters umis with non\-ACGT bases Expects formatted... +.TP +sb_filter +Filters reads with non\-matching sample barcodes... +.TP +sparse +Convert a CSV file to a sparse matrix with rows and... +.TP +subset_bamfile +Subset a SAM/BAM file, keeping only alignments from... +.TP +tagcount +Count up evidence for tagged molecules +.TP +umi_histogram +Counts the number of reads for each UMI Expects... +.IP +version +.SH AUTHOR +This manpage was written by Andreas Tille 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/umis/compare/19d1dcdaab09647e0cf51499f16dd268daf46b3a...fe00672bba0aef94d3e03c13525342c1238ff7f9 -- View it on GitLab: https://salsa.debian.org/med-team/umis/compare/19d1dcdaab09647e0cf51499f16dd268daf46b3a...fe00672bba0aef94d3e03c13525342c1238ff7f9 You're receiving this email because of your account on salsa.debian.org.
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