[med-svn] [augustus] 01/01: add first manpage for augustus
Sascha Steinbiss
sascha at steinbiss.name
Sat Mar 19 22:15:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository augustus.
commit d4d326b162617177b3c71122366ff33f408dbc0c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Mar 19 22:14:51 2016 +0000
add first manpage for augustus
---
debian/control | 3 +-
debian/manpages | 1 +
debian/mansrc/augustus.1 | 180 ++++++++++++++++++++++++++++++++++++++++++
debian/mansrc/augustus.1.adoc | 85 ++++++++++++++++++++
debian/rules | 1 +
5 files changed, 269 insertions(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index 6c6e745..b29f4e0 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
Build-Depends: debhelper (>= 9), libsqlite3-dev, libboost-iostreams-dev,
zlib1g-dev, libgsl-dev, liblpsolve55-dev,
- libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev
+ libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev,
+ asciidoctor
Standards-Version: 3.9.7
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/augustus.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/augustus.git
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..317f75d
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mansrc/*.1
diff --git a/debian/mansrc/augustus.1 b/debian/mansrc/augustus.1
new file mode 100644
index 0000000..4e62158
--- /dev/null
+++ b/debian/mansrc/augustus.1
@@ -0,0 +1,180 @@
+'\" t
+.\" Title: augustus
+.\" Author: [see the "AUTHORS" section]
+.\" Generator: Asciidoctor 1.5.4
+.\" Date: 2016-03-19
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "AUGUSTUS" "1" "2016-03-19" "\ \&" "\ \&"
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.ss \n[.ss] 0
+.nh
+.ad l
+.de URL
+\\$2 \(laURL: \\$1 \(ra\\$3
+..
+.if \n[.g] .mso www.tmac
+.LINKSTYLE blue R < >
+.SH "NAME"
+augustus \- a gene prediction tool
+.SH "SYNOPSIS"
+.sp
+\fBaugustus\fP [parameters] \-\-species=SPECIES queryfilename
+.SH "OPTIONS"
+.sp
+The mandatory option \(aqqueryfilename\(aq specifies the filename (including relative path) to the file containing the query sequence(s) in FASTA format.
+.sp
+SPECIES is an identifier for the species. Use \fB\-\-species=help\fP to see a list.
+.SS "Further parameters:"
+.sp
+\fB\-\-strand=both\fP, \fB\-\-strand=forward\fP or \fB\-\-strand=backward\fP
+.RS 4
+define the strand to search on
+.RE
+.sp
+\fB\-\-genemodel=genemodel\fP
+.RS 4
+where genemodel is one of:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+partial \- allow prediction of incomplete genes at the sequence boundaries (default)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+intronless \- only predict single\-exon genes like in prokaryotes and some eukaryotes
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+complete \- only predict complete genes
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+atleastone \- predict at least one complete gene
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+exactlyone \- predict exactly one complete gene
+.RE
+.RE
+.sp
+\fB\-\-singlestrand=true\fP
+.RS 4
+predict genes independently on each strand, allow overlapping genes on opposite strands.
+This option is turned off by default.
+.RE
+.sp
+*\-\-hintsfile=hintsfilenam*e
+.RS 4
+When this option is used the prediction considering hints (extrinsic information) is turned on.
+hintsfilename contains the hints in gff format.
+.RE
+.sp
+\fB\-\-AUGUSTUS_CONFIG_PATH=path\fP
+.RS 4
+path to config directory (if not specified as environment variable)
+.RE
+.sp
+\fB\-\-alternatives\-from\-evidence=true/false\fP
+.RS 4
+report alternative transcripts when they are suggested by hints
+.RE
+.sp
+\fB\-\-alternatives\-from\-sampling=true/false\fP
+.RS 4
+report alternative transcripts generated through probabilistic sampling
+.RE
+.sp
+\fB\-\-maxtracks=n\fP
+.RS 4
+For a description of these parameters see section 4 of README.TXT.
+.RE
+.sp
+\fB\-\-proteinprofile=filename\fP
+.RS 4
+When this option is used the prediction will consider the protein profile provided as parameter.
+The protein profile extension is described in section 7 of README.TXT.
+.RE
+.sp
+\fB\-\-progress=true\fP
+.RS 4
+show a progressmeter
+.RE
+.sp
+\fB\-\-gff3=on/off\fP
+.RS 4
+output in gff3 format
+.RE
+.sp
+\fB\-\-predictionStart=A\fP, \fB\-\-predictionEnd=B\fP
+.RS 4
+A and B define the range of the sequence for which predictions should be found.
+.RE
+.sp
+\fB\-\-UTR=on/off\fP
+.RS 4
+predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
+.RE
+.sp
+\fB\-\-noInFrameStop=true/false\fP
+.RS 4
+Do not report transcripts with in\-frame stop codons. Otherwise, intron\-spanning stop codons could occur. Default: false
+.RE
+.sp
+\fB\-\-noprediction=true/false\fP
+.RS 4
+If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
+.RE
+.sp
+\fB\-\-uniqueGeneId=true/false\fP
+.RS 4
+If true, output gene identifyers like this: seqname.gN
+.RE
+.sp
+\fB\-\-paramlist\fP
+.RS 4
+Show full list of supported parameters.
+.RE
+.SH "AUTHORS"
+.sp
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+.SH "ADDITIONAL DOCUMENTATION"
+.sp
+An exhaustive description can be found in the file /usr/share/augustus/README.TXT.
\ No newline at end of file
diff --git a/debian/mansrc/augustus.1.adoc b/debian/mansrc/augustus.1.adoc
new file mode 100644
index 0000000..0039e37
--- /dev/null
+++ b/debian/mansrc/augustus.1.adoc
@@ -0,0 +1,85 @@
+# augustus(1)
+
+## NAME
+
+augustus - a gene prediction tool
+
+## SYNOPSIS
+
+*augustus* [parameters] --species=SPECIES queryfilename
+
+## OPTIONS
+
+The mandatory option 'queryfilename' specifies the filename (including relative path) to the file containing the query sequence(s) in FASTA format.
+
+SPECIES is an identifier for the species. Use *--species=help* to see a list.
+
+### Further parameters:
+
+*--strand=both*, *--strand=forward* or *--strand=backward*::
+ define the strand to search on
+
+*--genemodel=genemodel*::
+ where genemodel is one of:
+ - partial - allow prediction of incomplete genes at the sequence boundaries (default)
+ - intronless - only predict single-exon genes like in prokaryotes and some eukaryotes
+ - complete - only predict complete genes
+ - atleastone - predict at least one complete gene
+ - exactlyone - predict exactly one complete gene
+
+*--singlestrand=true*::
+ predict genes independently on each strand, allow overlapping genes on opposite strands.
+ This option is turned off by default.
+
+*--hintsfile=hintsfilenam*e::
+ When this option is used the prediction considering hints (extrinsic information) is turned on.
+ hintsfilename contains the hints in gff format.
+
+*--AUGUSTUS_CONFIG_PATH=path*::
+ path to config directory (if not specified as environment variable)
+
+*--alternatives-from-evidence=true/false*::
+ report alternative transcripts when they are suggested by hints
+
+*--alternatives-from-sampling=true/false*::
+ report alternative transcripts generated through probabilistic sampling
+
+*--maxtracks=n*::
+ For a description of these parameters see section 4 of README.TXT.
+
+*--proteinprofile=filename*::
+ When this option is used the prediction will consider the protein profile provided as parameter.
+ The protein profile extension is described in section 7 of README.TXT.
+
+*--progress=true*::
+ show a progressmeter
+
+*--gff3=on/off*::
+ output in gff3 format
+
+*--predictionStart=A*, *--predictionEnd=B*::
+ A and B define the range of the sequence for which predictions should be found.
+
+*--UTR=on/off*::
+ predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
+
+*--noInFrameStop=true/false*::
+ Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur. Default: false
+
+*--noprediction=true/false*::
+ If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
+
+*--uniqueGeneId=true/false*::
+ If true, output gene identifyers like this: seqname.gN
+
+*--paramlist*::
+ Show full list of supported parameters.
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
+
diff --git a/debian/rules b/debian/rules
index 9b20d76..c98f92b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -29,6 +29,7 @@ override_dh_auto_build:
cd $(CURDIR)
cd auxprogs/joingenes && $(MAKE)
cd $(CURDIR)
+ asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
override_dh_auto_install:
mkdir -p debian/augustus/usr/bin
--
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