[med-svn] [repeatmasker-recon] 03/06: Try hard to get at least some minimum sensible manpages
Andreas Tille
tille at debian.org
Wed Apr 6 10:29:30 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/1.08-3
in repository repeatmasker-recon.
commit fc163fb80e10bbd72c2bd8db0bc032457505895c
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 6 12:20:43 2016 +0200
Try hard to get at least some minimum sensible manpages
---
debian/changelog | 2 +-
debian/mans/MSPCollect.1 | 19 +++++++++++++++++++
debian/mans/edgeredef.1 | 19 +++++++++++++++++++
debian/mans/eledef.1 | 18 ++++++++++++++++++
debian/mans/eleredef.1 | 21 +++++++++++++++++++++
debian/mans/famdef.1 | 15 +++++++++++++++
debian/mans/imagespread.1 | 13 +++++++++++++
debian/mans/repeatmasker-recon.1 | 26 ++++++++++++++++++++++++++
debian/repeatmasker-recon.manpages | 8 +-------
debian/rules | 12 ------------
10 files changed, 133 insertions(+), 20 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index d52b56f..2904363 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,7 +2,7 @@ repeatmasker-recon (1.08-3) UNRELEASED; urgency=medium
* Team upload
* Fix source URL
- * Do not create useless link to info page in manpages
+ * Provide better manpages
-- Andreas Tille <tille at debian.org> Tue, 02 Feb 2016 16:18:54 +0100
diff --git a/debian/mans/MSPCollect.1 b/debian/mans/MSPCollect.1
new file mode 100644
index 0000000..c26992a
--- /dev/null
+++ b/debian/mans/MSPCollect.1
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH MSPCOLLECT "1" "April 2016" "MSPCollect 1.08" "User Commands"
+.SH NAME
+MSPCollect \- convert a BLAST output into an MSP file
+.SH SYNOPSIS
+.B MSPCollect
+BLAST_output_file > name_of_your_MSP_file
+.SH DESCRIPTION
+Tool which converts a BLAST output into an
+MSP file, which is used by the repeatmasker-recon as input. In the MSP file,
+each MSP that BLAST reports is turned into a one-line summary in the
+following format:
+.IP
+score %iden start end query_name start end subject_name
+.SH SEE ALSO
+.IP
+zless /usr/share/doc/repeatmasker-recon/00README.gz
+.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/edgeredef.1 b/debian/mans/edgeredef.1
new file mode 100644
index 0000000..be0dc61
--- /dev/null
+++ b/debian/mans/edgeredef.1
@@ -0,0 +1,19 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH EDGEREDEF "1" "April 2016" "edgeredef 1.08" "User Commands"
+.SH NAME
+edgeredef \- repeatmasker helper to re-define edges
+.SH SYNOPSIS
+.B edgeredef
+seq_list start
+.SH DESCRIPTION
+This program belongs to repeatmasker-recon(1)
+.SH OPTIONS
+.TP
+seq_list
+the list of sequence names
+.TP
+start
+index of the element to start defining families
+The latter one is optional.
+.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/eledef.1 b/debian/mans/eledef.1
new file mode 100644
index 0000000..757e5a5
--- /dev/null
+++ b/debian/mans/eledef.1
@@ -0,0 +1,18 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH ELEDEF "1" "April 2016" "eledef 1.08" "User Commands"
+.SH NAME
+eledef \- repeatmasker helper to define elements
+.SH SYNOPSIS
+.B eledef
+\fIseq_list msp_file method cut_off\fR
+.SH DESCRIPTION
+This program belongs to repeatmasker-recon(1)
+.SH OPTIONS
+.TP
+\fImethod\fR
+choose 'single' or 'double'
+.TP
+\fIcutoff\fR
+optional
+.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/eleredef.1 b/debian/mans/eleredef.1
new file mode 100644
index 0000000..ee0a1f5
--- /dev/null
+++ b/debian/mans/eleredef.1
@@ -0,0 +1,21 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH ELEREDEF "1" "April 2016" "eleredef 1.08" "User Commands"
+.SH NAME
+eleredef \- repeatmasker helper to re-define elements
+.SH SYNOPSIS
+.B eleredef
+\fIseq_list start clan_ct\fR
+.SH DESCRIPTION
+This program belongs to repeatmasker-recon(1)
+.SH OPTIONS
+.TP
+\fIseq_list\fR
+list of sequence names
+.TP
+\fIstart\fR
+index of the element to start redefining (optional)
+.TP
+\fIclan_ct\fR
+number to start counting the number of clans (optional)
+.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/famdef.1 b/debian/mans/famdef.1
new file mode 100644
index 0000000..5ebdcb9
--- /dev/null
+++ b/debian/mans/famdef.1
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH FAMDEF "1" "April 2016" "famdef 1.08" "User Commands"
+.SH NAME
+famdef \- repeatmaker helper to define families
+.SH SYNOPSIS
+.B famdef
+\fIseq_list\fR
+.SH DESCRIPTION
+This program belongs to repeatmasker-recon(1)
+.SH OPTIONS
+.TP
+\fIseq_list\fR
+list of sequence names.
+.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/imagespread.1 b/debian/mans/imagespread.1
new file mode 100644
index 0000000..cb6bad0
--- /dev/null
+++ b/debian/mans/imagespread.1
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH IMAGESPREAD "1" "April 2016" "imagespread 1.08" "User Commands"
+.SH NAME
+imagespread \- repeat maker helper tool
+.SH SYNOPSIS
+.B imagespread
+\fIseq_name_list msp_list number_of_output_files\fR
+.SH DESCRIPTION
+This program belongs to repeatmasker-recon(1)
+.SH OPTIONS
+last parameter optional with default of 1
+.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/repeatmasker-recon.1 b/debian/mans/repeatmasker-recon.1
new file mode 100644
index 0000000..a627b49
--- /dev/null
+++ b/debian/mans/repeatmasker-recon.1
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH REPEATMASKER-RECON "1" "April 2016" "repeatmasker-recon 1.08" "User Commands"
+.SH NAME
+repeatmasker-recon \- finds repeat families from biological sequences
+.SH SYNOPSIS
+.B repeatmasker-recon
+seq_name_list_file MSP_file integer
+.SH DESCRIPTION
+The RECON package implements a de novo algorithm for the indentification
+of repeat families from biological sequences.
+.P
+The program implements an approach for the de novo identification and
+classification of repeat sequence families that is based on extensions
+to the usual approach of single linkage clustering of local pairwise
+alignments between genomic sequences. The extensions use multiple
+alignment information to define the boundaries of individual copies of
+the repeats and to distinguish homologous but distinct repeat element
+families. When tested on the human genome, this approach was able to
+properly identify and group known transposable elements. The program,
+should be useful for first-pass automatic classification of repeats in
+newly sequenced genomes.
+.SH SEE ALSO
+.IP
+zless /usr/share/doc/repeatmasker-recon/00README.gz
+.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/repeatmasker-recon.manpages b/debian/repeatmasker-recon.manpages
index d25b3e4..8c57398 100644
--- a/debian/repeatmasker-recon.manpages
+++ b/debian/repeatmasker-recon.manpages
@@ -1,7 +1 @@
-repeatmasker-recon.1
-MSPCollect.1
-edgeredef.1
-eledef.1
-eleredef.1
-famdef.1
-imagespread.1
+debian/mans/*.1
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
index feea39a..f00de2f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -34,19 +34,7 @@ override_dh_auto_install:
cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon
cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect
-
-override_dh_installman:
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/repeatmasker-recon > repeatmasker-recon.1
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/MSPCollect > MSPCollect.1
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/edgeredef > edgeredef.1
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/eledef > eledef.1
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/eleredef > eleredef.1
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/famdef > famdef.1
- help2man --version-string=$(DEB_UPSTREAM_VERSION) --no-info --no-discard-stderr debian/repeatmasker-recon/usr/bin/imagespread > imagespread.1
- dh_installman
-
override_dh_clean:
cd src; make clean
rm -rf bin
- rm -f *.1
dh_clean
--
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