[med-svn] [pbsuite] 09/12: Add manpage stubs as pointers to more detailed documentation

[Afif Elghraoui]

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afif pushed a commit to branch master
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commit eaa5c109abc2af833bb91f392f4ebc07b9d8e5bc
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Feb 27 00:13:25 2016 -0800

    Add manpage stubs as pointers to more detailed documentation
---
 debian/man/Honey.1      | 21 +++++++++++++++++++++
 debian/man/Jelly.1      | 15 +++++++++++++++
 debian/pbhoney.links    |  1 +
 debian/pbhoney.manpages |  1 +
 debian/pbjelly.links    |  1 +
 debian/pbjelly.manpages |  1 +
 6 files changed, 40 insertions(+)

diff --git a/debian/man/Honey.1 b/debian/man/Honey.1
new file mode 100644
index 0000000..2b40006
--- /dev/null
+++ b/debian/man/Honey.1
@@ -0,0 +1,21 @@
+.TH HONEY 1 "February 2016"
+.SH NAME
+Honey \- genomic structural variation discovery
+.SH SYNOPSIS
+.B Honey
+.RI { subcommand } [ options ]
+.SH DESCRIPTION
+PBHoney is an implementation of two variant-identification
+approaches designed to exploit the high mappability of long reads
+(i.e., greater than 10,000 bp). PBHoney considers both intra-read
+discordance and soft-clipped tails of long reads to identify
+structural variants.
+.SH OPTIONS
+For a complete description, see the help menu
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.SH SEE ALSO
+.BR blasr (1)
+.br
+/usr/share/doc/pbhoney/HoneyReadme.txt
diff --git a/debian/man/Jelly.1 b/debian/man/Jelly.1
new file mode 100644
index 0000000..f2e37f9
--- /dev/null
+++ b/debian/man/Jelly.1
@@ -0,0 +1,15 @@
+.TH JELLY 1 "February 2016"
+.SH NAME
+Jelly \- genome assembly upgrading tool
+.SH DESCRIPTION
+PBJelly is a highly automated pipeline that aligns long sequencing
+reads (such as PacBio RS reads or long 454 reads in fasta format)
+to high-confidence draft assembles. PBJelly fills or reduces as
+many captured gaps as possible to produce upgraded draft genomes.
+.SH OPTIONS
+For a complete description, see the help menu
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.SH SEE ALSO
+/usr/share/doc/pbjelly/JellyReadme.txt
diff --git a/debian/pbhoney.links b/debian/pbhoney.links
index 61f5021..3ce7724 100644
--- a/debian/pbhoney.links
+++ b/debian/pbhoney.links
@@ -1,2 +1,3 @@
 /usr/lib/python2.7/dist-packages/pbsuite/honey/Honey.py	/usr/bin/Honey
 /usr/bin/Honey						/usr/bin/Honey.py
+/usr/share/man/man1/Honey.1				/usr/share/man/man1/Honey.py.1
diff --git a/debian/pbhoney.manpages b/debian/pbhoney.manpages
new file mode 100644
index 0000000..2ad779c
--- /dev/null
+++ b/debian/pbhoney.manpages
@@ -0,0 +1 @@
+debian/man/Honey.1
diff --git a/debian/pbjelly.links b/debian/pbjelly.links
index c1cc2d0..ffb9eaa 100644
--- a/debian/pbjelly.links
+++ b/debian/pbjelly.links
@@ -1,2 +1,3 @@
 /usr/lib/python2.7/dist-packages/pbsuite/jelly/Jelly.py	/usr/bin/Jelly
 /usr/bin/Jelly						/usr/bin/Jelly.py
+/usr/share/man/man1/Jelly.1				/usr/share/man/man1/Jelly.py.1
\ No newline at end of file
diff --git a/debian/pbjelly.manpages b/debian/pbjelly.manpages
new file mode 100644
index 0000000..17d5de7
--- /dev/null
+++ b/debian/pbjelly.manpages
@@ -0,0 +1 @@
+debian/man/Jelly.1

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