[med-svn] [augustus] 02/06: fix man pages

Sascha Steinbiss satta at debian.org
Sat Jul 29 05:14:01 UTC 2017 

This is an automated email from the git hooks/post-receive script.

satta pushed a commit to branch master
in repository augustus.

commit 52489a95f2933ac512c90a7755b6b45582452af7
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Jul 28 20:56:25 2017 +0200

    fix man pages
---
 debian/mansrc/{aln2wig.1.adoc_ => aln2wig.1.adoc} |  0
 debian/mansrc/bam2wig.1.adoc                      | 31 +++++++++++++++
 debian/mansrc/compileSpliceCands.1.adoc           | 42 ++++++++++++++++++++
 debian/mansrc/consensusFinder.1.adoc              | 47 -----------------------
 debian/mansrc/curve2hints.1.adoc_                 | 47 -----------------------
 debian/patches/buildflags.patch                   |  4 +-
 debian/rules                                      | 23 +++++++----
 7 files changed, 91 insertions(+), 103 deletions(-)

diff --git a/debian/mansrc/aln2wig.1.adoc_ b/debian/mansrc/aln2wig.1.adoc
similarity index 100%
rename from debian/mansrc/aln2wig.1.adoc_
rename to debian/mansrc/aln2wig.1.adoc
diff --git a/debian/mansrc/bam2wig.1.adoc b/debian/mansrc/bam2wig.1.adoc
new file mode 100644
index 0000000..4af0fa5
--- /dev/null
+++ b/debian/mansrc/bam2wig.1.adoc
@@ -0,0 +1,31 @@
+# bam2wig(1)
+
+## NAME
+
+bam2wig - convert BAM to WIG
+
+## SYNOPSIS
+
+*bam2wig* [-r region] [-t trackname] <in.bam>
+
+## OPTIONS
+
+File needs to be sorted by Reference ID (i.e. target name)
+Use 'samtools sort <in.bam>' to such effect.
+
+###  Parameters:
+
+*-r*::
+  Allows to specify a target region, e.g. 'chr3L:10-250'
+  This option can only be used if an index file exists, see: samtools index
+
+*-t*::
+  string provided as track name
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
diff --git a/debian/mansrc/compileSpliceCands.1.adoc b/debian/mansrc/compileSpliceCands.1.adoc
new file mode 100644
index 0000000..7293f55
--- /dev/null
+++ b/debian/mansrc/compileSpliceCands.1.adoc
@@ -0,0 +1,42 @@
+# compileSpliceCands(1)
+
+## NAME
+
+compileSpliceCands - Find introns parsing a set of exon candidates in GFF format
+
+## SYNOPSIS
+
+*compileSpliceCands* -f <splice candidates filename> -g <genome filename>
+
+## OPTIONS
+
+###  Parameters:
+
+*-f* <filename>::
+  potential splice sites in gff format
+
+*-g* <filename>::
+  genome file in fasta format
+
+*-c* <integer>::
+	defines the number of potential splice site every potential splice site itself is compared with
+
+*-t* <float>::
+	has to be between 0 and 1 and  defines how much the average coverage may differ
+
+*-m* <integer>::
+	defines how many bases around the splice site should be checked
+
+*-d*::
+	enables debugging output
+
+*-i* <integer>::
+	maximum length an Intron can be, default 500000 (human genome)
+
+## AUTHORS
+
+AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
+
+## ADDITIONAL DOCUMENTATION
+
+An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
diff --git a/debian/mansrc/consensusFinder.1.adoc b/debian/mansrc/consensusFinder.1.adoc
deleted file mode 100644
index 6610fd4..0000000
--- a/debian/mansrc/consensusFinder.1.adoc
+++ /dev/null
@@ -1,47 +0,0 @@
-# consensusFinder(1)
-
-## NAME
-
-consensusFinder - consensus finder
-
-## SYNOPSIS
-
-*consensusFinder* input_fasta_file [options]
-
-## OPTIONS
-
-*-l*::
-  pattern length
-
-*-p*::
-  p-value for finding the significant strings
-
-*-d*::
-  delta to find the relevant strings
-
-*-s*::
-  starting position
-
-*-e*::
-  ending position
-
-*-m*::
-  no. of mismatches to consider while finding neighbours
-
-*-c*::
-  string to consider for analysis
-
-*-n*::
-  specify the number of consensus patterns to store
-
-*-t*::
-  print the histogram
-
-## AUTHORS
-
-AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
-
-## ADDITIONAL DOCUMENTATION
-
-An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
-
diff --git a/debian/mansrc/curve2hints.1.adoc_ b/debian/mansrc/curve2hints.1.adoc_
deleted file mode 100644
index 22bee26..0000000
--- a/debian/mansrc/curve2hints.1.adoc_
+++ /dev/null
@@ -1,47 +0,0 @@
-# curve2hints(1)
-
-## NAME
-
-curve2hints - tool to make exon segmentation and grouping the exons together to form AUGUSTUS hints
-
-## SYNOPSIS
-
-*curve2hints* --in=file --outexons=out.gff --c=int --s=float
-
-## OPTIONS
-
-*--in=s*::
-   iput file is single file containing tracks in wig format
-
-*--outexons=s*::
-   file for the output segmentaion
-
-*--c*::
-   specify the threshold to distinguish between introns and exons in terms of coverage depths (default 4)
-
-*--s*::
-   specify the ratio *(1-lambda1)/(1-lambda2)* It should be >1 (default 1.12)
-
-*--z*::
-  specify the chunk size (default value 50000)
-
-*--r*::
-  To enable re-estimation of distribution from the output produced
-
-*--train_file*::
-  Specify the gff file to be used for training the distributions.It should contain the position of both introns and exons
-
-*--bed_file*::
-  Specify the output bedfile which contains the position of gene jumps (default: output.bed)
-
-*--augustus_hints*::
-  Specify the output augustus hint file(default: augustus_hints.gff)
-
-## AUTHORS
-
-AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
-
-## ADDITIONAL DOCUMENTATION
-
-An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.
-
diff --git a/debian/patches/buildflags.patch b/debian/patches/buildflags.patch
index 8f30392..26ad0c6 100644
--- a/debian/patches/buildflags.patch
+++ b/debian/patches/buildflags.patch
@@ -30,11 +30,11 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  
  .cc.o:
 -	$(CC) -c $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< $(INCLS)
-+	$(CC) -c $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< $(INCLS)
++	$(CC) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $< $(INCLS)
  
  homGeneMapping: main.cc $(OBJS)
 -	$(CC) $(CFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS)  $(LIBS)
-+	$(CC) $(CXXFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS)  $(LIBS)
++	$(CC) $(CXXFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS) $(LDFLAGS)  $(LIBS)
  	cp homGeneMapping ../../../bin/homGeneMapping
  
  clean:
diff --git a/debian/rules b/debian/rules
index 508c374..7cc40f7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -35,11 +35,16 @@ joingenes: bin
 
 override_dh_auto_clean:
 	$(MAKE) -C auxprogs/bam2hints clean
-	$(MAKE) -C auxprogs/homGeneMapping/src clean
+	$(MAKE) -C auxprogs/homGeneMapping clean
 	$(MAKE) -C auxprogs/joingenes clean
+	$(MAKE) -C auxprogs/aln2wig clean
+	$(MAKE) -C auxprogs/bam2wig clean
+	$(MAKE) -C auxprogs/checkTargetSortedness clean
+	$(MAKE) -C auxprogs/compileSpliceCands clean
+	$(MAKE) -C auxprogs/filterBam clean
 	rm -rf bin
 
-override_dh_auto_build: bam2hints homGeneMapping checkTargetSortedness joingenes bin
+override_dh_auto_build: aln2wig bam2hints bam2wig checkTargetSortedness compileSpliceCands filterBam homGeneMapping joingenes
 	dh_auto_build
 	asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
 
@@ -50,18 +55,22 @@ override_dh_auto_install:
 	mkdir -p         debian/augustus/usr/bin
 	install bin/*    debian/augustus/usr/bin
 	install auxprogs/checkTargetSortedness/checkTargetSortedness \
-	                 debian/augustus/usr/bin
+                   debian/augustus/usr/bin
+	install auxprogs/bam2wig/bam2wig \
+                   debian/augustus/usr/bin
+	install auxprogs/compileSpliceCands/compileSpliceCands \
+                   debian/augustus/usr/bin
 	install auxprogs/homGeneMapping/src/homGeneMapping \
-	                 debian/augustus/usr/bin
+                   debian/augustus/usr/bin
 	install auxprogs/joingenes/joingenes \
 	                 debian/augustus/usr/bin
 	mkdir -p         debian/augustus/usr/share/augustus
 	cp -r scripts    debian/augustus/usr/share/augustus
 	chmod -R -x      debian/augustus/usr/share/augustus/scripts/*
-	rm -f            debian/augustus/usr/share/augustus/scripts/*.patch
-	chmod +x         debian/augustus/usr/share/augustus/scripts/checkUTR \
-	                 debian/augustus/usr/share/augustus/scripts/*.pl* \
+	rm -rf           debian/augustus/usr/share/augustus/scripts/*.patch \
 	                 debian/augustus/usr/share/augustus/scripts/aln2wig
+	chmod +x         debian/augustus/usr/share/augustus/scripts/checkUTR \
+	                 debian/augustus/usr/share/augustus/scripts/*.pl*
 	mkdir -p         debian/augustus-doc/usr/share/doc/augustus
 	cp README*       debian/augustus-doc/usr/share/doc/augustus
 	cp docs/*.txt    debian/augustus-doc/usr/share/doc/augustus

-- 
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