[med-svn] [deepnano] 01/04: added manpages

[Çağrı ULAŞ]

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cagriulas-guest pushed a commit to branch master
in repository deepnano.

commit 5cdd3acd8ac73ead36e827563d3250ce13d0d51e
Author: Çağrı ULAŞ <cagriulas at gmail.com>
Date:   Wed Feb 22 01:54:06 2017 +0300

    added manpages
---
 debian/deepnano.manpages                |  1 +
 debian/deepnano_basecall.1              | 66 +++++++++++++++++++++++++++++++++
 debian/deepnano_basecall_no_metrichor.1 | 59 +++++++++++++++++++++++++++++
 3 files changed, 126 insertions(+)

diff --git a/debian/deepnano.manpages b/debian/deepnano.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/deepnano.manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/deepnano_basecall.1 b/debian/deepnano_basecall.1
new file mode 100644
index 0000000..4493004
--- /dev/null
+++ b/debian/deepnano_basecall.1
@@ -0,0 +1,66 @@
+.TH DEEPNANO_BASECALL "1" "February 2017" "deepnano_basecall 0.0+20110617" "User Commands"
+.SH NAME
+deepnano_basecall \- basecaller for Oxford Nanopore MinION reads based on deep recurrent neural networks
+.SH SYNOPSIS
+\fBusage:\fR deepnano_basecall [\fIARGS\fP] [reads [reads ...]]
+.SH DESCRIPTION
+.SS "positional arguments:"
+.IP
+reads
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+.TP
+\fB\-\-template_net\fR TEMPLATE_NET
+path to network which basecalls template (has reasonable default)
+.HP
+.TP
+\fB\-\-complement_net\fR COMPLEMENT_NET
+path to network which basecalls complement (has reasonable default)
+.HP
+.TP
+\fB\-\-big_net\fR BIG_NET
+path to network which basecalls 2D (has reasonable default)
+.HP
+.TP
+\fB\-\-timing\fR
+if set, display timing information for each read
+.TP
+\fB\-\-type\fR TYPE
+One of: template, complement, 2d, all, use comma to
+separate multiple options, eg.: template,complement
+type of basecalling output (defaults to all)
+.HP
+.TP
+\fB\-\-output\fR OUTPUT
+output filename
+.HP
+.TP
+\fB\-\-output_orig\fR
+if set, outputs also Metrichor basecalls
+.TP
+\fB\-\-directory\fR DIRECTORY
+Directory where read files are stored
+.SH EXAMPLES
+.TP
+For SQK-MAP-006 chemistry just use:
+\fBOMP_NUM_THREADS=1 deepnano_basecall <list of fast5 files>\fP
+
+or
+
+\fBOMP_NUM_THREADS=1 deepnano_basecall --directory <directory with reads>\fP
+
+It outputs basecalls for template, complement and 2D into file named output.fasta.
+.TP
+For SQK-MAP-005 chemistry use:
+\fBOMP_NUM_THREADS=1 deepnano_basecall \-\-template_net nets_data/map5temp.npz \-\-complement_net nets_data/map5comp.npz \-\-big_net nets_data/map5-2d.npz <list of fast5 files>\fP
+.SH "SEE ALSO"
+.PP
+\fBdeepnano_basecall_no_metrichor\fR(1)
+.SH AUTHOR
+This manpage was written by Çağrı ULAŞ for the Debian distribution and can be used for any other usage of the program.
+.SH BUGS
+Report bugs to <https://bitbucket.org/vboza/deepnano/issues>
+
diff --git a/debian/deepnano_basecall_no_metrichor.1 b/debian/deepnano_basecall_no_metrichor.1
new file mode 100644
index 0000000..132708a
--- /dev/null
+++ b/debian/deepnano_basecall_no_metrichor.1
@@ -0,0 +1,59 @@
+.TH DEEPNANO_BASECALL_NO_METRICHOR "1" "February 2017" "deepnano_basecall_no_metrichor 0.0+20110617" "User Commands"
+.SH NAME
+deepnano_basecall_no_metrichor \- basecaller for Oxford Nanopore MinION reads based on deep recurrent neural networks
+.SH SYNOPSIS
+\fBusage:\fR deepnano_basecall_no_metrichor [\fIARGS\fP] [reads [reads ...]]
+.SH DESCRIPTION
+.SS "positional arguments:"
+.IP
+reads
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+.TP
+\fB\-\-template_net\fR TEMPLATE_NET
+path to network which basecalls template (has reasonable default)
+.HP
+.TP
+\fB\-\-complement_net\fR COMPLEMENT_NET
+path to network which basecalls complement (has reasonable default)
+.HP
+.TP
+\fB\-\-big_net\fR BIG_NET
+path to network which basecalls 2D (has reasonable default)
+.TP
+\fB\-\-max_2d_length\fR MAX_2D_LENGTH
+Max length for 2d basecall
+.TP
+\fB\-\-type\fR TYPE
+One of: template, complement, 2d, all, use comma to
+separate multiple options, eg.: template,complement
+type of basecalling output (defaults to all)
+.HP
+.TP
+\fB\-\-output\fR OUTPUT
+output filename
+.TP
+\fB\-\-directory\fR DIRECTORY
+Directory where read files are stored
+.TP
+\fB\-\-watch\fR WATCH
+Watched directory
+.SH EXAMPLES
+.TP
+Using without metrichor:
+\fBOMP_NUM_THREADS=1 deepnano_basecall_no_metrichor <list of fast5 files>\fP
+.TP
+If you want to watch a directory (watchdog must be installed)
+
+\fBOMP_NUM_THREADS=1 deepnano_basecall_no_metrichor --watch <directory name>\fP
+.SH "SEE ALSO"
+.PP
+\fBdeepnano_basecall\fR(1)
+.SH AUTHOR
+This manpage was written by Çağrı ULAŞ for the Debian distribution and can be used for any other usage of the program.
+.SH BUGS
+Report bugs to <https://bitbucket.org/vboza/deepnano/issues>
+

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