[med-svn] [bio-rainbow] 02/02: rename_binary

[Olivier Sallou]

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osallou pushed a commit to branch patch-queue/master
in repository bio-rainbow.

commit a0c43009ed59ad1f8cdd19fee15563be754312b6
Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Date:   Mon Aug 17 14:17:14 2015 +0000

    rename_binary
    
    
    Gbp-Pq: Name rename_binary.patch
---
 Makefile   |  6 +++---
 README.txt | 14 +++++++-------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/Makefile b/Makefile
index 77fb275..ffdb580 100644
--- a/Makefile
+++ b/Makefile
@@ -16,9 +16,9 @@ GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.
 	$(CC) -c $(CFLAGS) $(DFLAGS) $< -o $@
 
 #all: rainbow rbasm rbmergetag ezmsim 
-all: rainbow ezmsim rbasm
+all: bio-rainbow ezmsim rbasm
 
-rainbow: main.o  divide.o file_reader.o asm_R2.o mergectg.o cluster.o
+bio-rainbow: main.o  divide.o file_reader.o asm_R2.o mergectg.o cluster.o
 	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(GLIBS)
 
 rbasm: asm_R2.o rbasm_main.o file_reader.o
@@ -48,7 +48,7 @@ rbasm_main.o: rbasm_main.c asm_R2.h string.h vector.h hashset.h \
 stdaln.o: stdaln.c stdaln.h
 
 clean:
-	rm -f *.o *.gcda *.gcno *.gcov gmon.out rainbow rbasm ezmsim rbmergetag *.exe
+	rm -f *.o *.gcda *.gcno *.gcov gmon.out bio-rainbow rbasm ezmsim rbmergetag *.exe
 
 clear:
 	rm -f *.o *.gcda *.gcno *.gcov gmon.out
diff --git a/README.txt b/README.txt
index d4fd3dd..0c74fe8 100644
--- a/README.txt
+++ b/README.txt
@@ -16,12 +16,12 @@ Usage of Rainbow package
 ========================
 EXAMPLE: a typical use of Rainbow step by step
 
-	rainbow cluster -1 1.fq  -2 2.fq > rbcluster.out 2> log
-	rainbow div -i rbcluster.out -o rbdiv.out
-	rainbow merge -o rbasm.out -a -i rbdiv.out -N500
+	bio-rainbow cluster -1 1.fq  -2 2.fq > rbcluster.out 2> log
+	bio-rainbow div -i rbcluster.out -o rbdiv.out
+	bio-rainbow merge -o rbasm.out -a -i rbdiv.out -N500
 
-The final output file of 'rainbow merge -a' is based on the final merged
-clusters. Each cluster has been locally assembled by 'rainbow merge -a'. For
+The final output file of 'bio-rainbow merge -a' is based on the final merged
+clusters. Each cluster has been locally assembled by 'bio-rainbow merge -a'. For
 each cluster, rainbow outputs all assembled contigs seperated by '//' for each
 record:
 E clusterID
@@ -53,8 +53,8 @@ respectively
 select_best_rbcontig_plus_read1.pl, as select_best_rbcontig.pl, it  extracts the longest contig for each cluster. Besides, it also outputs the read1. If read1 overlaps with the contig, it joins the two as a whole. If read1 does not overlap with the contig, it pads 10 'X' to join the read1 and the contig, thus generating a long contig. 
 
 ----------------------------------------------------------------------------------
-rainbow 2.0.3 -- <ruanjue at gmail.com, chongzechen at gmail.com>
-Usage: rainbow <cmd> [options]
+bio-rainbow 2.0.3 -- <ruanjue at gmail.com, chongzechen at gmail.com>
+Usage: bio-rainbow <cmd> [options]
 
  cluster
   Input  File Format: paired fasta/fastq file(s)

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