# HG changeset patch
# User rogerngo
# Date 1337142244 14400
# Node ID cfe16849421e2dea1e7f745f43d5b828d150a85c
# Parent  f8037d6c5f14c46a0777d29e45791526cdc565d4
iAssembler readme uploaded

diff -r f8037d6c5f14 -r cfe16849421e iAssembler_README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iAssembler_README.txt	Wed May 16 00:24:04 2012 -0400
@@ -0,0 +1,73 @@
+iAssembler tools for Galaxy
+
+	iAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs. 
+	The pipeline gives much higher accuracy in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated 
+	error corrections of mis-assemblies. 
+
+	iAssembler first performs iterative assemblies using MIRA and CAP3 (default: four cycles of MIRA assemblies followed by one CAP3 assembly) to correct 
+	assembly errors (mostly sequences derived from the same transcript fail to be assembled together) which occur frequently in just one round of assembly. 
+
+	The program then performs post-assembly quality checking by 
+	1) aligning each EST sequence to its corresponding unigene sequence to identify mis-assemblies; and 
+	2) performing all-verus-all pair-wise sequence alignments of unigenes to identify sequences derived from same transcripts that fail to be assembled together. 
+
+	The identified mis-assemblies are then corrected by the program automatically.
+
+	http://bioinfo.bti.cornell.edu/tool/iAssembler/
+
+	Citation:
+	Zheng Y, Zhao L, Gao J, Fei Z. (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453
+
+Galaxy XML and Perl wrapper script written by: Roger Ngo, Sam Min and Todd H. Oakley, UCSB
+
+Included files in this package:
+
+* iAssembler.xml - Galaxy XML tool for iAssembler 1.3
+* iAssembler_wrapper.pl - Wrapper script for Galaxy XML tool
+* increment.txt - File required by iAssembler_wrapper.pl
+* iAssembler_README - Documentation file
+
+Note: iAssembler.pl MUST BE modified in lines 254-258 due to a bug preventing the program from working in the Galaxy platform.
+
+Pre-Installation:
+
+iAssembler 1.3 must be installed on the Galaxy user account. In order for the Galaxy tool wrapper to work, the iAssembler.pl
+script must be modified on lines 254-258.
+
+FROM:
+
+my $version_file = $working_dir."/mira_version";
+system("$program_bin_dir/mira | head > $version_file");
+
+TO:
+
+my $version_file = $working_dir."/mira_version";
+system("$program_bin_dir/mira > $working_dir/out");
+system("head  $working_dir/out > $version_file");
+
+
+Installation Instructions:
+
+1. Copy the iAssembler folder to a directory in your Galaxy user account.
+
+2. Copy iAssembler.xml, iAssembler_wrapper.pl and increment.txt to a folder in /galaxy-dist/tools/
+
+Note: increment.txt and iAssembler_wrapper.pl MUST be in the same directory.
+
+3. In iAssembler_wrapper.pl, modify the $iAssemblerBinPath to point to the iAssembler 1.3 directory in your
+Galaxy user account and $iAssemblerToolPath to the path of the wrapper.
+
+By default they have already been assigned as:
+
+my $iAssemblerBinPath = '/labdata/nfs/galaxy/pkgs/iAssembler';
+my $iAssemblerToolPath = '/labdata/nfs/galaxy/galaxy-dist/tools/iAssembler';
+
+4. Add the Galaxy tool information to tool_conf.xml in /galaxy-dist/
+
+5. Restart Galaxy using 
+
+./run.sh --stop-daemon
+
+and then
+
+./run.sh --reload --daemon
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