[med-svn] [SCM] fastx-toolkit branch, master, updated. debian/0.0.13.1-1-7-g613eea3

[Andreas Tille]

The following commit has been merged in the master branch:
commit 613eea3e3e7002550b09c245fbcade93c34e27a0
Author: Andreas Tille <tille at debian.org>
Date:   Thu Apr 26 16:17:46 2012 +0200

    Add hint about useful link in README.Debian
    Use result from help2man command line as file because it simply breaks the build process otherwise mysterically

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..aec6e30
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,16 @@
+FastX Toolkit for Debian
+------------------------
+
+The manpages in this package are autogenerated via help2man which does
+not always result in a pretty layout.  To get a better layout as well
+as some big picture about all tools it is advisable to visit
+
+   http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
+
+You might also like to have a look at
+
+   http://hannonlab.cshl.edu/fastx_toolkit/galaxy.html
+
+
+ -- Andreas Tille <tille at debian.org>  Wed, 25 Apr 2012 22:31:55 +0200
+
diff --git a/debian/changelog b/debian/changelog
index 3747b06..66613d1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -13,6 +13,7 @@ fastx-toolkit (0.0.13.1-2) UNRELEASED; urgency=low
      - convert from cdbs to dh to finally enable hardening flags
      - use help2man to creat manpages where possible
   * debhelper 9 (control+compat) to support hardening flags
+  * debian/README.Debian: Add hint for useful web page
 
  -- Andreas Tille <tille at debian.org>  Wed, 25 Apr 2012 22:31:55 +0200
 
diff --git a/debian/fastq_quality_trimmer.1 b/debian/fastq_quality_trimmer.1
new file mode 100644
index 0000000..90e82cd
--- /dev/null
+++ b/debian/fastq_quality_trimmer.1
@@ -0,0 +1,35 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.8.
+.TH FASTQ_QUALITY_TRIMMER "1" "April 2012" "fastq_quality_trimmer 0.0.13.1" "User Commands"
+.SH NAME
+fastq_quality_trimmer \- Filters sequences based on quality
+.SH DESCRIPTION
+usage: fastq_quality_trimmer [\-h] [\-v] [\-t N] [\-l N] [\-z] [\-i INFILE] [\-o OUTFILE]
+Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gordon at cshl.edu)
+.TP
+[\-h]
+= This helpful help screen.
+.TP
+[\-t N]
+= Quality threshold \- nucleotides with lower
+.IP
+quality will be trimmed (from the end of the sequence).
+.TP
+[\-l N]
+= Minimum length \- sequences shorter than this (after trimming)
+.IP
+will be discarded. Default = 0 = no minimum length.
+.TP
+[\-z]
+= Compress output with GZIP.
+.TP
+[\-i INFILE]
+= FASTQ input file. default is STDIN.
+.IP
+[\-o OUTFILE] = FASTQ output file. default is STDOUT.
+[\-v]         = Verbose \- report number of sequences.
+.TP
+If [\-o] is specified,
+report will be printed to STDOUT.
+.IP
+If [\-o] is not specified (and output goes to STDOUT),
+report will be printed to STDERR.
diff --git a/debian/rules b/debian/rules
index 39f45b4..7b572ef 100755
--- a/debian/rules
+++ b/debian/rules
@@ -50,6 +50,8 @@ override_dh_installman:
 #	help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
 #	   --name='Filters sequences based on quality' \
 #	   $(bindir)/fastq_quality_trimmer > $(mandir)/fastq_quality_trimmer .1
+# lets simply use what works perfectly at command line
+	dh_installman debian/fastq_quality_trimmer.1
 
 	help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
 	   --name='Convert FASTQ files to FASTA files' \

-- 
FASTQ/A short-reads pre-processing tools