[med-svn] [bio-rainbow] 09/11: update README about renaming

[Olivier Sallou]

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

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

commit 685a99cde15ea2854536db44025634b8a607d7f2
Author: Olivier Sallou <osallou at debian.org>
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 -- <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)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bio-rainbow.git