[med-svn] [SCM] fastx-toolkit branch, master, updated. debian/0.0.13.1-1-6-g47a526d
Andreas Tille
tille at debian.org
Thu Apr 26 14:06:09 UTC 2012
The following commit has been merged in the master branch:
commit 47a526d85d9d66c7c0f6888ec2879eb730d154a9
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 26 16:04:41 2012 +0200
"Wrote" close to all manpages with the exception of one single page where help2man mysteriosely failed. A manual postprocessing of these pages could be helpful in some cases but it would help when working offline in any case this way.
diff --git a/debian/changelog b/debian/changelog
index 6d00d6c..3747b06 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,10 +4,14 @@ fastx-toolkit (0.0.13.1-2) UNRELEASED; urgency=low
- Added myself to Uploaders
- Standards-Version: 3.9.3 (no changes needed)
- Add missing dependencies of Perl scripts
+ - Add Build-Depends help2man
+ - Add Perl modules also ad Build-Depends to enable also
+ running help2man on Perl scripts
* debian/patches/gcc-4.7.patch: Fix build issue with gcc-4.7
Closes: #667161
- * debian/rules: convert from cdbs to dh to finally enable hardening
- flags
+ * debian/rules:
+ - 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
-- Andreas Tille <tille at debian.org> Wed, 25 Apr 2012 22:31:55 +0200
diff --git a/debian/control b/debian/control
index 553c8d0..526e5a0 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9), autotools-dev, pkg-config, libgtextutils-dev
+Build-Depends: debhelper (>= 9), autotools-dev, pkg-config, libgtextutils-dev,
+ help2man, libgd-graph-perl, libperlio-gzip-perl
Standards-Version: 3.9.3
Vcs-Browser: http://git.debian.org/?p=debian-med/fastx-toolkit.git
Vcs-Git: git://git.debian.org/debian-med/fastx-toolkit.git
diff --git a/debian/manpages_see_also b/debian/manpages_see_also
new file mode 100644
index 0000000..a3e1415
--- /dev/null
+++ b/debian/manpages_see_also
@@ -0,0 +1,8 @@
+.SH SEE ALSO
+The quality of this automaticly generated manpage might be
+insufficient. It is suggested to visit
+.IP
+http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
+.P
+to get a better layout as well as an overview about connected
+FastX tools.
diff --git a/debian/rules b/debian/rules
index 641748f..39f45b4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,10 @@
#!/usr/bin/make -f
pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+ver := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
+
+mandir := $(CURDIR)/debian/$(pkg)/usr/share/man/man1
+bindir := $(CURDIR)/debian/$(pkg)/usr/bin
%:
dh $@
@@ -11,3 +15,92 @@ override_dh_install:
override_dh_installchangelogs:
dh_installchangelogs -k NEWS
+
+# Does not help to detect the dependencies for substitution variable ${perl:Depends} :-(
+#override_dh_perl:
+# dh_perl /usr/bin
+
+override_dh_installman:
+ mkdir -p $(mandir)
+ # The name strings are obtained from
+ # http://hannonlab.cshl.edu/fastx_toolkit/ (Section "Available Tools")
+ # and
+ # http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='changes the width of sequences line in a FASTA file' \
+ $(bindir)/fasta_formatter > $(mandir)/fasta_formatter.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='Convets FASTA sequences from/to RNA/DNA' \
+ $(bindir)/fasta_nucleotide_changer > $(mandir)/fasta_nucleotide_changer.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name="Masks nucleotides with 'N' (or other character) based on quality" \
+ $(bindir)/fastq_masker > $(mandir)/fastq_masker.1
+
+ # FIXME: The tool `fasta_quality_converter` was NOT described at the URLs above
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='Converts sequences based on quality' \
+ $(bindir)/fastq_quality_converter > $(mandir)/fastq_quality_converter.1
+
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='Filters sequences based on quality' \
+ $(bindir)/fastq_quality_filter > $(mandir)/fastq_quality_filter.1
+
+# FIXME: For some very strange reason this conversion fails
+#
+# help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+# --name='Filters sequences based on quality' \
+# $(bindir)/fastq_quality_trimmer > $(mandir)/fastq_quality_trimmer .1
+
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='Convert FASTQ files to FASTA files' \
+ $(bindir)/fastq_to_fasta > $(mandir)/fastq_to_fasta.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTQ/A Artifacts Filter' \
+ $(bindir)/fastx_artifacts_filter > $(mandir)/fastx_artifacts_filter.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Clipper' \
+ $(bindir)/fastx_clipper > $(mandir)/fastx_clipper.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Collapser' \
+ $(bindir)/fastx_collapser > $(mandir)/fastx_collapser.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTX Statistics' \
+ $(bindir)/fastx_quality_stats > $(mandir)/fastx_quality_stats.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Renamer' \
+ $(bindir)/fastx_renamer > $(mandir)/fastx_renamer.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTQ/A Reverse Complement' \
+ $(bindir)/fastx_reverse_complement > $(mandir)/fastx_reverse_complement.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Trimmer' \
+ $(bindir)/fastx_trimmer > $(mandir)/fastx_trimmer.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Uncollapser' \
+ $(bindir)/fastx_uncollapser > $(mandir)/fastx_uncollapser.1
+
+ # Perl scripts add the full path to usage advise which needs to be removed
+ # The script fasta_clipping_histogram.pl does not feature a '-h' option
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' -h '' \
+ --name='Create a Linker Clipping Information Histogram' \
+ $(bindir)/fasta_clipping_histogram.pl | \
+ sed -e 's?^usage: .*\([^/]\+\.pl\)?usage: \1?' \
+ > $(mandir)/fasta_clipping_histogram.pl.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTX Barcode Splitter' \
+ $(bindir)/fastx_barcode_splitter.pl | \
+ sed -e 's?^usage: .*\([^/]\+\.pl\)?usage: \1?' \
+ > $(mandir)/fastx_barcode_splitter.pl.1
+
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='Solexa-Quality BoxPlot plotter' \
+ $(bindir)/fastq_quality_boxplot_graph.sh > $(mandir)/fastq_quality_boxplot_graph.sh.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Nucleotide Distribution Plotter' \
+ $(bindir)/fastx_nucleotide_distribution_graph.sh > $(mandir)/fastx_nucleotide_distribution_graph.sh.1
+ help2man --no-info --no-discard-stderr --version-string='$(ver)' --help-option='-h' \
+ --name='FASTA/Q Nucleotide Distribution Plotter' \
+ $(bindir)/fastx_nucleotide_distribution_line_graph.sh > $(mandir)/fastx_nucleotide_distribution_line_graph.sh.1
+
+ for man in `find $(mandir) "*.1"` ; do cat debian/manpages_see_also >> $$man ; done
+
--
FASTQ/A short-reads pre-processing tools
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