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commit a0c43009ed59ad1f8cdd19fee15563be754312b6 Author: Debian Med Packaging Team <[email protected]> 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 -- <[email protected], [email protected]> -Usage: rainbow <cmd> [options] +bio-rainbow 2.0.3 -- <[email protected], [email protected]> +Usage: bio-rainbow <cmd> [options] cluster Input File Format: paired fasta/fastq file(s) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bio-rainbow.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
