[med-svn] [Git][med-team/picopore][master] 4 commits: Synopsis, install README, copyright times
Andreas Tille
gitlab at salsa.debian.org
Sun Jun 7 08:07:57 BST 2020
Andreas Tille pushed to branch master at Debian Med / picopore
Commits:
63f6ae69 by Andreas Tille at 2020-06-07T08:03:12+02:00
Synopsis, install README, copyright times
- - - - -
965ad71d by Andreas Tille at 2020-06-07T08:58:30+02:00
Add manpages
- - - - -
04323bcd by Andreas Tille at 2020-06-07T09:02:51+02:00
Section: python
- - - - -
d9c2dc4e by Andreas Tille at 2020-06-07T09:07:33+02:00
Add upstream metadata
- - - - -
10 changed files:
- debian/control
- debian/copyright
- + debian/createmanpages
- + debian/docs
- + debian/man/picopore-realtime.1
- + debian/man/picopore-rename.1
- + debian/man/picopore-test.1
- + debian/man/picopore.1
- + debian/manpages
- + debian/upstream/metadata
Changes:
=====================================
debian/control
=====================================
@@ -30,9 +30,10 @@ Description: lossless compression of Nanopore files
Package: python3-picopore
Architecture: all
+Section: python
Depends: ${python3:Depends}, ${misc:Depends},
hdf5-tools
-Description: lossless compression of Nanopore files
+Description: lossless compression of Nanopore files (Python3 module)
The Nanopore is a device to determine the sequences of single moleculres
of DNA. No amplification. The output is gigantic and tools like this
one help to reduce it.
=====================================
debian/copyright
=====================================
@@ -3,7 +3,7 @@ Upstream-Name: picopore
Source: https://github.com/scottgigante/picopore
Files: *
-Copyright: Scott Gigante <scottgigante at gmail.com>
+Copyright: 2016-2019 Scott Gigante <scottgigante at gmail.com>
License: GPL-3+
Files: debian/*
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,46 @@
+#!/bin/sh
+MANDIR=debian/man
+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=" --help" \
+ --name="reducing the size of an Oxford Nanopore Technologies dataset without losing any data" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=picopore-realtime
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="monitors a directory for new reads and compresses them in real time" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=picopore-rename
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="renaming groups and datasets within Oxford Nanopore Technologies FAST5 files" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=picopore-test
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name="compresses to temporary files and checks that all datasets and attributes are equal" \
+ --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 @@
+README*
=====================================
debian/man/picopore-realtime.1
=====================================
@@ -0,0 +1,64 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH PICOPORE-REALTIME "1" "June 2020" "picopore-realtime 1.2.0" "User Commands"
+.SH NAME
+picopore-realtime \- monitors a directory for new reads and compresses them in real time
+.SH SYNOPSIS
+.B picopore\-realtime
+[\-h] \fB\-\-mode\fR {lossless,deep\-lossless,raw} [\-\-revert]
+[\-\-fastq] [\-\-summary] [\-\-manual STR] [\-v] [\-y]
+[\-t INT] [\-\-prefix STR] [\-\-skip\-root]
+[\-\-print\-every INT]
+[input [input ...]]
+.SH DESCRIPTION
+A tool for reducing the size of an Oxford Nanopore Technologies dataset without losing any data
+.PP
+picopore\-realtime monitors a directory for new reads and compresses them in real time
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+input
+list of directories or fast5 files to shrink
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-mode\fR {lossless,deep\-lossless,raw}
+choose compression mode
+.TP
+\fB\-\-revert\fR
+reverts files to original size (lossless modes only)
+.TP
+\fB\-\-fastq\fR, \fB\-\-no\-fastq\fR
+retain FASTQ data (raw mode only) (Default: \fB\-\-fastq\fR)
+.TP
+\fB\-\-summary\fR, \fB\-\-no\-summary\fR
+retain summary data (raw mode only) (Default: \fB\-\-nosummary\fR)
+.TP
+\fB\-\-manual\fR STR
+manually remove only groups whose paths contain STR
+(raw mode only, regular expressions permitted,
+overrides defaults)
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show version number and exit
+.TP
+\fB\-y\fR
+skip confirm step
+.TP
+\fB\-t\fR INT, \fB\-\-threads\fR INT
+number of threads (Default: 1)
+.TP
+\fB\-\-prefix\fR STR
+add prefix to output files to prevent overwrite
+.TP
+\fB\-\-skip\-root\fR, \fB\-\-no\-skip\-root\fR
+ignore files in root input directories for albacore
+realtime compression (Default: \fB\-\-no\-skip\-root\fR)
+.TP
+\fB\-\-print\-every\fR INT
+print a dot every approximately INT files, or \fB\-1\fR to
+silence (Default: 100)
+.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/man/picopore-rename.1
=====================================
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH PICOPORE-RENAME "1" "June 2020" "picopore-rename 1.2.0" "User Commands"
+.SH NAME
+picopore-rename \- renaming groups and datasets within Oxford Nanopore Technologies FAST5 files
+.SH SYNOPSIS
+.b picopore\-rename
+[\-h] \fB\-p\fR PATTERN \fB\-r\fR REPLACEMENT [\-v] [\-y] [\-t INT]
+[\-\-prefix STR] [\-\-skip\-root] [\-\-print\-every INT]
+[input [input ...]]
+.SH DESCRIPTION
+A tool for renaming groups and datasets within Oxford Nanopore Technologies
+FAST5 files
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+input
+list of directories or fast5 files to shrink
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-p\fR PATTERN, \fB\-\-pattern\fR PATTERN
+String or regex to replace
+.TP
+\fB\-r\fR REPLACEMENT, \fB\-\-replacement\fR REPLACEMENT
+String or regex replacement for PATTERN
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show version number and exit
+.TP
+\fB\-y\fR
+skip confirm step
+.TP
+\fB\-t\fR INT, \fB\-\-threads\fR INT
+number of threads (Default: 1)
+.TP
+\fB\-\-prefix\fR STR
+add prefix to output files to prevent overwrite
+.TP
+\fB\-\-skip\-root\fR, \fB\-\-no\-skip\-root\fR
+ignore files in root input directories for albacore
+realtime compression (Default: \fB\-\-no\-skip\-root\fR)
+.TP
+\fB\-\-print\-every\fR INT
+print a dot every approximately INT files, or \fB\-1\fR to
+silence (Default: 100)
+.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/man/picopore-test.1
=====================================
@@ -0,0 +1,63 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH PICOPORE-TEST "1" "June 2020" "picopore-test 1.2.0" "User Commands"
+.SH NAME
+picopore-test \- compresses to temporary files and checks that all datasets and attributes are equal
+.SH SYNOPSIS
+.B picopore\-test
+[\-h] \fB\-\-mode\fR {lossless,deep\-lossless,raw} [\-\-revert]
+[\-\-fastq] [\-\-summary] [\-\-manual STR] [\-v] [\-y] [\-t INT]
+[\-\-prefix STR] [\-\-skip\-root] [\-\-print\-every INT]
+[input [input ...]]
+.SH DESCRIPTION
+A tool for reducing the size of an Oxford Nanopore Technologies dataset without losing any data
+.PP
+picopore\-test compresses to temporary files and checks that all datasets and attributes are equal (lossless modes only)
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+input
+list of directories or fast5 files to shrink
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-mode\fR {lossless,deep\-lossless,raw}
+choose compression mode
+.TP
+\fB\-\-revert\fR
+reverts files to original size (lossless modes only)
+.TP
+\fB\-\-fastq\fR, \fB\-\-no\-fastq\fR
+retain FASTQ data (raw mode only) (Default: \fB\-\-fastq\fR)
+.TP
+\fB\-\-summary\fR, \fB\-\-no\-summary\fR
+retain summary data (raw mode only) (Default: \fB\-\-nosummary\fR)
+.TP
+\fB\-\-manual\fR STR
+manually remove only groups whose paths contain STR
+(raw mode only, regular expressions permitted,
+overrides defaults)
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show version number and exit
+.TP
+\fB\-y\fR
+skip confirm step
+.TP
+\fB\-t\fR INT, \fB\-\-threads\fR INT
+number of threads (Default: 1)
+.TP
+\fB\-\-prefix\fR STR
+add prefix to output files to prevent overwrite
+.TP
+\fB\-\-skip\-root\fR, \fB\-\-no\-skip\-root\fR
+ignore files in root input directories for albacore
+realtime compression (Default: \fB\-\-no\-skip\-root\fR)
+.TP
+\fB\-\-print\-every\fR INT
+print a dot every approximately INT files, or \fB\-1\fR to
+silence (Default: 100)
+.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/man/picopore.1
=====================================
@@ -0,0 +1,71 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15.
+.TH PICOPORE "1" "June 2020" "picopore 1.2.0" "User Commands"
+.SH NAME
+picopore \- reducing the size of an Oxford Nanopore Technologies dataset without losing any data
+.SH SYNOPSIS
+.B picopore
+[\-h] \fB\-\-mode\fR {lossless,deep\-lossless,raw} [\-\-revert] [\-\-fastq]
+[\-\-summary] [\-\-manual STR] [\-v] [\-y] [\-t INT] [\-\-prefix STR]
+[\-\-skip\-root] [\-\-print\-every INT]
+[input [input ...]]
+.SH DESCRIPTION
+A tool for reducing the size of an Oxford Nanopore Technologies dataset without losing any data
+.SH OPTIONS
+.SS "See also:"
+.TP
+picopore\-realtime
+monitors a directory for new reads and compresses them in real time
+.TP
+picopore\-test
+compresses to temporary files and checks that all datasets and attributes are equal (lossless modes only)
+.TP
+picopore\-rename
+renames groups and datasets within FAST5 files
+.SS "positional arguments:"
+.TP
+input
+list of directories or fast5 files to shrink
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-mode\fR {lossless,deep\-lossless,raw}
+choose compression mode
+.TP
+\fB\-\-revert\fR
+reverts files to original size (lossless modes only)
+.TP
+\fB\-\-fastq\fR, \fB\-\-no\-fastq\fR
+retain FASTQ data (raw mode only) (Default: \fB\-\-fastq\fR)
+.TP
+\fB\-\-summary\fR, \fB\-\-no\-summary\fR
+retain summary data (raw mode only) (Default: \fB\-\-nosummary\fR)
+.TP
+\fB\-\-manual\fR STR
+manually remove only groups whose paths contain STR
+(raw mode only, regular expressions permitted,
+overrides defaults)
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show version number and exit
+.TP
+\fB\-y\fR
+skip confirm step
+.TP
+\fB\-t\fR INT, \fB\-\-threads\fR INT
+number of threads (Default: 1)
+.TP
+\fB\-\-prefix\fR STR
+add prefix to output files to prevent overwrite
+.TP
+\fB\-\-skip\-root\fR, \fB\-\-no\-skip\-root\fR
+ignore files in root input directories for albacore
+realtime compression (Default: \fB\-\-no\-skip\-root\fR)
+.TP
+\fB\-\-print\-every\fR INT
+print a dot every approximately INT files, or \fB\-1\fR to
+silence (Default: 100)
+.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/manpages
=====================================
@@ -0,0 +1 @@
+debian/man/*.1
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,17 @@
+Reference:
+ Author: Scott Gigante
+ Title: >
+ Picopore: A tool for reducing the storage size of Oxford Nanopore
+ Technologies datasets without loss of functionality
+ Journal: F1000Res
+ Year: 2017
+ Volume: 6:
+ Pages: 227
+ DOI: 10.12688/f1000research.11022.3
+ PMID: 28413619
+ PMCID: PMC5365225
+ URL: https://f1000research.com/articles/6-227/v1
+ eprint: https://f1000research.com/articles/6-227/v1/pdf?article_uuid=7f39a108-1f9a-432d-bbf6-57b2acb9bbc2
+Registry:
+ - Name: conda:bioconda
+ Entry: picopore
View it on GitLab: https://salsa.debian.org/med-team/picopore/-/compare/8e497fd253f7bd56ff1580fba27e11471992e201...d9c2dc4e1e7149608e98ca4826562649192ad8ee
--
View it on GitLab: https://salsa.debian.org/med-team/picopore/-/compare/8e497fd253f7bd56ff1580fba27e11471992e201...d9c2dc4e1e7149608e98ca4826562649192ad8ee
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