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commit 685a99cde15ea2854536db44025634b8a607d7f2 Author: Olivier Sallou <[email protected]> Date: Mon Aug 17 14:16:56 2015 +0000 update README about renaming --- debian/patches/rename_binary.patch | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/debian/patches/rename_binary.patch b/debian/patches/rename_binary.patch index e76e412..b5d324c 100644 --- a/debian/patches/rename_binary.patch +++ b/debian/patches/rename_binary.patch @@ -21,3 +21,34 @@ clear: rm -f *.o *.gcda *.gcno *.gcov gmon.out +--- a/README.txt ++++ b/README.txt +@@ -16,12 +16,12 @@ + ======================== + 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 @@ + 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
