[med-svn] r12990 - trunk/packages/meme/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-02-12 15:24:33 +0000 (Tue, 12 Feb 2013)
New Revision: 12990

Modified:
   trunk/packages/meme/trunk/debian/rules
Log:
Had a hard time to help2man those tools that output to stderr - I wished help2man would be a bit more flexible ...


Modified: trunk/packages/meme/trunk/debian/rules
===================================================================
--- trunk/packages/meme/trunk/debian/rules	2013-02-12 14:10:52 UTC (rev 12989)
+++ trunk/packages/meme/trunk/debian/rules	2013-02-12 15:24:33 UTC (rev 12990)
@@ -65,6 +65,7 @@
 
 override_dh_installman:
 	mkdir -p $(mandir)
+	mkdir -p debian/tmp-man
 	for var in `ls debian/tmp/usr/bin/*` ; do \
 	    if head -n 1 $${var} | grep -q '^#!/usr/bin/perl' ; then pod2man $${var} > $(mandir)/`basename $${var}`.1 ; fi ; \
 	done
@@ -83,15 +84,41 @@
 	help2man --no-info  --help-option="''" --no-discard-stderr \
 	    --name='Load all motifs within a MEME motif file and write to eps' --version-string="$(version)" \
                  $(CURDIR)/debian/$(pkg)/usr/bin/ceqlogo > $(mandir)/ceqlogo.1
-# The next two are leading to "Error opening file"
-#	help2man --no-info  --help-option="''" --no-discard-stderr \
-#	    --name='Converts a multiple alignment in clustalw format into a FASTA file' --version-string="$(version)" \
-#                 $(CURDIR)/debian/$(pkg)/usr/bin/clustalw2fasta > $(mandir)/clustalw2fasta.1
-#	help2man --no-info  --help-option="''" --no-discard-stderr \
-#	    --name='Converts a multiple alignment in clustalw format into a Phylip file' --version-string="$(version)" \
-#                 $(CURDIR)/debian/$(pkg)/usr/bin/clustalw2phylip > $(mandir)/clustalw2phylip.1
+# Very dirty trick to drain information via help2man even if binary outputs to stderr
+	binname=clustalw2fasta ; \
+	tmpbin=$(CURDIR)/debian/tmp-man/$$binname ; \
+	echo "#!/bin/sh" > $$tmpbin ; echo "cat <<EOT" >> $$tmpbin; $(CURDIR)/debian/$(pkg)/usr/bin/$$binname 2>> $$tmpbin; chmod 755 $$tmpbin; \
+	help2man --no-info  --help-option="''" --no-discard-stderr \
+	    --name='Converts a multiple alignment in clustalw format into a FASTA file' --version-string="$(version)" \
+                 $$tmpbin > $(mandir)/$${binname}.1
+	binname=clustalw2phylip ; \
+	tmpbin=$(CURDIR)/debian/tmp-man/$$binname ; \
+	echo "#!/bin/sh" > $$tmpbin ; echo "cat <<EOT" >> $$tmpbin; $(CURDIR)/debian/$(pkg)/usr/bin/$$binname 2>> $$tmpbin; chmod 755 $$tmpbin; \
+	help2man --no-info  --help-option="''" --no-discard-stderr \
+	    --name='Converts a multiple alignment in clustalw format into a Phylip file' --version-string="$(version)" \
+                 $$tmpbin > $(mandir)/$${binname}.1
+	help2man --no-info  --help-option="''" --no-discard-stderr \
+	    --name='computes the distribution of priors from a file in MEME PSP format' --version-string="$(version)" \
+                 $(CURDIR)/debian/$(pkg)/usr/bin/compute-prior-dist > $(mandir)/compute-prior-dist.1
+# Very dirty trick to drain information via help2man even if binary outputs to stderr
+	binname=create-priors ; \
+	tmpbin=$(CURDIR)/debian/tmp-man/$$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
+	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 > $(mandir)/draw-mhmm.1
+	help2man --no-info  --help-option="''" --no-discard-stderr \
+	    --name='some component of MEME package without specific description' --version-string="$(version)" \
+                 $(CURDIR)/debian/$(pkg)/usr/bin/dust > $(mandir)/dust.1
+	help2man --no-info  --help-option="''" --no-discard-stderr \
+	    --name='read a sequence file in FASTA format and writes it to standard out' --version-string="$(version)" \
+                 $(CURDIR)/debian/$(pkg)/usr/bin/fasta-io > $(mandir)/fasta-io.1
 	# Remove those manpages with zero bytes where pod2man failed in doing a proper job
 	find $(mandir) -size 0 -delete
+	rm -rf debian/tmp-man
 	dh_installman
 
 override_dh_clean:
@@ -107,6 +134,7 @@
 	rm -f etc/motif_db.csv etc/gomo_db.csv etc/fasta_db.csv etc/logging.conf
 	# Remove Makefiles of libxml2 and libxslt
 	find src -name Makefile -delete
+	find src -type d -name .deps | xargs rm -rf
 
 #XXX Disable testing temporarily to save time
 override_dh_auto_test: