[med-svn] [centrifuge] 02/02: Add manpages
Andreas Tille
tille at debian.org
Sat Jan 6 10:59:24 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository centrifuge.
commit fb6f3b14fce05d916e7db9fcdbf4571e5861648f
Author: Andreas Tille <tille at debian.org>
Date: Sat Jan 6 11:52:45 2018 +0100
Add manpages
---
debian/bin/centrifuge-sort-nt | 1 -
debian/createmanpages | 46 +++++++++++++++++++++++++++++++++
debian/manpages | 1 +
debian/mans/centrifuge-build.1 | 18 +++++++++++++
debian/mans/centrifuge-compress.1 | 8 ++++++
debian/mans/centrifuge-download.1 | 53 +++++++++++++++++++++++++++++++++++++++
debian/mans/centrifuge-inspect.1 | 18 +++++++++++++
debian/mans/centrifuge.1 | 10 ++++++++
8 files changed, 154 insertions(+), 1 deletion(-)
diff --git a/debian/bin/centrifuge-sort-nt b/debian/bin/centrifuge-sort-nt
deleted file mode 120000
index 397b56e..0000000
--- a/debian/bin/centrifuge-sort-nt
+++ /dev/null
@@ -1 +0,0 @@
-centrifuge
\ No newline at end of file
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..ade8494
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,46 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=centrifuge
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='rapid and memory-efficient system for classification of DNA sequences' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=centrifuge-build
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='building index on all complete bacterial and viral genomes' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=centrifuge-compress
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='genome compression in the database construction' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=centrifuge-download
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='centrifuge helper to download databases' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=centrifuge-inspect
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='inspecting the centrifuge index' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/centrifuge-build.1 b/debian/mans/centrifuge-build.1
new file mode 100644
index 0000000..9bb0067
--- /dev/null
+++ b/debian/mans/centrifuge-build.1
@@ -0,0 +1,18 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CENTRIFUGE-BUILD "1" "December 2017" "centrifuge-build 1.0.3~beta" "User Commands"
+.SH NAME
+centrifuge-build \- building index on all complete bacterial and viral genomes
+.SH DESCRIPTION
+.SS "Traceback (most recent call last):"
+.IP
+File "./centrifuge\-build", line 79, in <module>
+.IP
+main()
+.IP
+File "./centrifuge\-build", line 76, in main
+.IP
+os.execv(build_bin_spec, argv)
+.PP
+OSError: [Errno 2] No such file or directory
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/centrifuge-compress.1 b/debian/mans/centrifuge-compress.1
new file mode 100644
index 0000000..61af33b
--- /dev/null
+++ b/debian/mans/centrifuge-compress.1
@@ -0,0 +1,8 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CENTRIFUGE-COMPRESS "1" "December 2017" "centrifuge-compress 1.0.3~beta" "User Commands"
+.SH NAME
+centrifuge-compress \- genome compression in the database construction
+.SH DESCRIPTION
+USAGE: perl centrifuge\-compress.pl path_to_download_files path_to_taxnonomy [\-map header_to_taxid_map \fB\-o\fR compressed \fB\-noCompress\fR \fB\-t\fR 1 \fB\-maxG\fR 50000000 \fB\-noDustmasker]\fR
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/centrifuge-download.1 b/debian/mans/centrifuge-download.1
new file mode 100644
index 0000000..b398afc
--- /dev/null
+++ b/debian/mans/centrifuge-download.1
@@ -0,0 +1,53 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CENTRIFUGE-DOWNLOAD "1" "December 2017" "centrifuge-download 1.0.3~beta" "User Commands"
+.SH NAME
+centrifuge-download \- centrifuge helper to download databases
+.SH DESCRIPTION
+centrifuge\-download [<options>] <database>
+.PP
+ARGUMENT
+.TP
+<database>
+One of refseq, genbank, contaminants or taxonomy:
+.TP
+\- use refseq or genbank for genomic sequences,
+\- contaminants gets contaminant sequences from UniVec and EmVec,
+\- taxonomy for taxonomy mappings.
+.PP
+COMMON OPTIONS
+.TP
+\fB\-o\fR <directory>
+Folder to which the files are downloaded. Default: '.'.
+.TP
+\fB\-P\fR <# of threads>
+Number of processes when downloading (uses xargs). Default: '1'
+.SS "WHEN USING database refseq OR genbank:"
+.TP
+\fB\-d\fR <domain>
+What domain to download. One or more of bacteria, viral, archaea, fungi, protozoa, invertebrate, plant, vertebrate_mammalian, vertebrate_other (comma separated).
+.TP
+\fB\-a\fR <assembly level>
+Only download genomes with the specified assembly level. Default: 'Complete Genome'.
+.TP
+\fB\-c\fR <refseq category>
+Only download genomes in the specified refseq category. Default: any.
+.TP
+\fB\-t\fR <taxids>
+Only download the specified taxonomy IDs, comma separated. Default: any.
+.TP
+\fB\-r\fR
+Download RNA sequences, too.
+.TP
+\fB\-u\fR
+Filter unplaced sequences.
+.TP
+\fB\-m\fR
+Mask low\-complexity regions using dustmasker. Default: off.
+.TP
+\fB\-l\fR
+Modify header to include taxonomy ID. Default: off.
+.TP
+\fB\-g\fR
+Download GI map.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/centrifuge-inspect.1 b/debian/mans/centrifuge-inspect.1
new file mode 100644
index 0000000..541112f
--- /dev/null
+++ b/debian/mans/centrifuge-inspect.1
@@ -0,0 +1,18 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CENTRIFUGE-INSPECT "1" "December 2017" "centrifuge-inspect 1.0.3~beta" "User Commands"
+.SH NAME
+centrifuge-inspect \- inspecting the centrifuge index
+.SH DESCRIPTION
+.SS "Traceback (most recent call last):"
+.IP
+File "./centrifuge\-inspect", line 55, in <module>
+.IP
+main()
+.IP
+File "./centrifuge\-inspect", line 51, in main
+.IP
+os.execv(inspect_bin_spec, arguments)
+.PP
+OSError: [Errno 2] No such file or directory
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/centrifuge.1 b/debian/mans/centrifuge.1
new file mode 100644
index 0000000..7086bb8
--- /dev/null
+++ b/debian/mans/centrifuge.1
@@ -0,0 +1,10 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CENTRIFUGE "1" "December 2017" "centrifuge 1.0.3~beta" "User Commands"
+.SH NAME
+centrifuge \- rapid and memory-efficient system for classification of DNA sequences
+.SH DESCRIPTION
+(ERR): Expected centrifuge to be in same directory with centrifuge\-class:
+/home/andreas/debian\-maintain/alioth/debian\-med_git/0_prospective/centrifuge/
+Exiting now ...
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
--
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