[med-svn] r12991 - in trunk/packages/meme/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-02-12 15:40:45 +0000 (Tue, 12 Feb 2013)
New Revision: 12991

Added:
   trunk/packages/meme/trunk/debian/patches/what-is-entries-for-pod2man.patch
Modified:
   trunk/packages/meme/trunk/debian/patches/series
   trunk/packages/meme/trunk/debian/rules
Log:
Further work to increase manpages


Modified: trunk/packages/meme/trunk/debian/patches/series
===================================================================
--- trunk/packages/meme/trunk/debian/patches/series	2013-02-12 15:24:33 UTC (rev 12990)
+++ trunk/packages/meme/trunk/debian/patches/series	2013-02-12 15:40:45 UTC (rev 12991)
@@ -3,3 +3,4 @@
 fix_installer_paths
 #broken and most probably unneeded, see Remark inside the file# fix_plib_path
 perl-include.patch
+what-is-entries-for-pod2man.patch

Added: trunk/packages/meme/trunk/debian/patches/what-is-entries-for-pod2man.patch
===================================================================
--- trunk/packages/meme/trunk/debian/patches/what-is-entries-for-pod2man.patch	                        (rev 0)
+++ trunk/packages/meme/trunk/debian/patches/what-is-entries-for-pod2man.patch	2013-02-12 15:40:45 UTC (rev 12991)
@@ -0,0 +1,29 @@
+Author: Andreas Tille <tille at debian.org>
+Description: Fix .pl files to enable proper manpages via pod2man
+
+--- a/scripts/beeml2meme.pl.in
++++ b/scripts/beeml2meme.pl.in
+@@ -17,6 +17,10 @@ use Fcntl qw(O_RDONLY);
+ use Getopt::Long;
+ use Pod::Usage;
+ 
++=head1 NAME
++
++beeml2meme - Convert a file containing list of TFBS motif matrices from BEEML
++
+ =head1 SYNOPSIS
+ 
+ beeml2meme [options] <matrix file>
+--- a/scripts/nmica2meme.pl.in
++++ b/scripts/nmica2meme.pl.in
+@@ -19,6 +19,10 @@ use Pod::Usage;
+ use XML::Simple;
+ use Data::Dumper;
+ 
++=head1 NAME
++
++nmica2meme - Convert a file containing list of TFBS motif matrices from
++
+ =head1 SYNOPSIS
+ 
+ nmica2meme [options]

Modified: trunk/packages/meme/trunk/debian/rules
===================================================================
--- trunk/packages/meme/trunk/debian/rules	2013-02-12 15:24:33 UTC (rev 12990)
+++ trunk/packages/meme/trunk/debian/rules	2013-02-12 15:40:45 UTC (rev 12991)
@@ -100,22 +100,30 @@
 	help2man --no-info  --help-option="''" --no-discard-stderr \
 	    --name='computes the distribution of priors from a file in MEME PSP format' --version-string="$(version)" \
                  $(CURDIR)/debian/$(pkg)/usr/bin/compute-prior-dist > $(mandir)/compute-prior-dist.1
-# Very dirty trick to drain information via help2man even if binary outputs to stderr
 	binname=create-priors ; \
 	tmpbin=$(CURDIR)/debian/tmp-man/$$binname ; \
 	echo "#!/bin/sh" > $$tmpbin ; echo "cat <<EOT" >> $$tmpbin; $(CURDIR)/debian/$(pkg)/usr/bin/$$binname 2>> $$tmpbin; chmod 755 $$tmpbin; \
 	help2man --no-info  --help-option="''" --no-discard-stderr \
 	    --name='converts numeric values defined with respect to one or more DNA sequences into a probabilistic prior' --version-string="$(version)" \
                  $$tmpbin > $(mandir)/$${binname}.1
+	binname=draw-mhmm ; \
+	tmpbin=$(CURDIR)/debian/tmp-man/$$binname ; \
+	echo "#!/bin/sh" > $$tmpbin ; echo "cat <<EOT" >> $$tmpbin; $(CURDIR)/debian/$(pkg)/usr/bin/$$binname 2>> $$tmpbin; chmod 755 $$tmpbin; \
 	help2man --no-info  --help-option="''" --no-discard-stderr \
 	    --name='convert a given Meta-MEME hidden Markov model into a format suitable for input to graphviz' --version-string="$(version)" \
-                 $(CURDIR)/debian/$(pkg)/usr/bin/draw-mhmm > $(mandir)/draw-mhmm.1
+                 $$tmpbin > $(mandir)/$${binname}.1
+	binname=dust ; \
+	tmpbin=$(CURDIR)/debian/tmp-man/$$binname ; \
+	echo "#!/bin/sh" > $$tmpbin ; echo "cat <<EOT" >> $$tmpbin; $(CURDIR)/debian/$(pkg)/usr/bin/$$binname 2>> $$tmpbin; chmod 755 $$tmpbin; \
 	help2man --no-info  --help-option="''" --no-discard-stderr \
 	    --name='some component of MEME package without specific description' --version-string="$(version)" \
-                 $(CURDIR)/debian/$(pkg)/usr/bin/dust > $(mandir)/dust.1
+                 $$tmpbin > $(mandir)/$${binname}.1
+	binname=fasta-io ; \
+	tmpbin=$(CURDIR)/debian/tmp-man/$$binname ; \
+	echo "#!/bin/sh" > $$tmpbin ; echo "cat <<EOT" >> $$tmpbin; $(CURDIR)/debian/$(pkg)/usr/bin/$$binname 2>> $$tmpbin; chmod 755 $$tmpbin; \
 	help2man --no-info  --help-option="''" --no-discard-stderr \
 	    --name='read a sequence file in FASTA format and writes it to standard out' --version-string="$(version)" \
-                 $(CURDIR)/debian/$(pkg)/usr/bin/fasta-io > $(mandir)/fasta-io.1
+                 $$tmpbin > $(mandir)/$${binname}.1
 	# Remove those manpages with zero bytes where pod2man failed in doing a proper job
 	find $(mandir) -size 0 -delete
 	rm -rf debian/tmp-man