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