Mercurial > repos > rogerngo > iassembler
comparison iAssembler_README.txt @ 3:cfe16849421e draft
iAssembler readme uploaded
| author | rogerngo |
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| date | Wed, 16 May 2012 00:24:04 -0400 |
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| 2:f8037d6c5f14 | 3:cfe16849421e |
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| 1 iAssembler tools for Galaxy | |
| 2 | |
| 3 iAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs. | |
| 4 The pipeline gives much higher accuracy in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated | |
| 5 error corrections of mis-assemblies. | |
| 6 | |
| 7 iAssembler first performs iterative assemblies using MIRA and CAP3 (default: four cycles of MIRA assemblies followed by one CAP3 assembly) to correct | |
| 8 assembly errors (mostly sequences derived from the same transcript fail to be assembled together) which occur frequently in just one round of assembly. | |
| 9 | |
| 10 The program then performs post-assembly quality checking by | |
| 11 1) aligning each EST sequence to its corresponding unigene sequence to identify mis-assemblies; and | |
| 12 2) performing all-verus-all pair-wise sequence alignments of unigenes to identify sequences derived from same transcripts that fail to be assembled together. | |
| 13 | |
| 14 The identified mis-assemblies are then corrected by the program automatically. | |
| 15 | |
| 16 http://bioinfo.bti.cornell.edu/tool/iAssembler/ | |
| 17 | |
| 18 Citation: | |
| 19 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 | |
| 20 | |
| 21 Galaxy XML and Perl wrapper script written by: Roger Ngo, Sam Min and Todd H. Oakley, UCSB | |
| 22 | |
| 23 Included files in this package: | |
| 24 | |
| 25 * iAssembler.xml - Galaxy XML tool for iAssembler 1.3 | |
| 26 * iAssembler_wrapper.pl - Wrapper script for Galaxy XML tool | |
| 27 * increment.txt - File required by iAssembler_wrapper.pl | |
| 28 * iAssembler_README - Documentation file | |
| 29 | |
| 30 Note: iAssembler.pl MUST BE modified in lines 254-258 due to a bug preventing the program from working in the Galaxy platform. | |
| 31 | |
| 32 Pre-Installation: | |
| 33 | |
| 34 iAssembler 1.3 must be installed on the Galaxy user account. In order for the Galaxy tool wrapper to work, the iAssembler.pl | |
| 35 script must be modified on lines 254-258. | |
| 36 | |
| 37 FROM: | |
| 38 | |
| 39 my $version_file = $working_dir."/mira_version"; | |
| 40 system("$program_bin_dir/mira | head > $version_file"); | |
| 41 | |
| 42 TO: | |
| 43 | |
| 44 my $version_file = $working_dir."/mira_version"; | |
| 45 system("$program_bin_dir/mira > $working_dir/out"); | |
| 46 system("head $working_dir/out > $version_file"); | |
| 47 | |
| 48 | |
| 49 Installation Instructions: | |
| 50 | |
| 51 1. Copy the iAssembler folder to a directory in your Galaxy user account. | |
| 52 | |
| 53 2. Copy iAssembler.xml, iAssembler_wrapper.pl and increment.txt to a folder in /galaxy-dist/tools/ | |
| 54 | |
| 55 Note: increment.txt and iAssembler_wrapper.pl MUST be in the same directory. | |
| 56 | |
| 57 3. In iAssembler_wrapper.pl, modify the $iAssemblerBinPath to point to the iAssembler 1.3 directory in your | |
| 58 Galaxy user account and $iAssemblerToolPath to the path of the wrapper. | |
| 59 | |
| 60 By default they have already been assigned as: | |
| 61 | |
| 62 my $iAssemblerBinPath = '/labdata/nfs/galaxy/pkgs/iAssembler'; | |
| 63 my $iAssemblerToolPath = '/labdata/nfs/galaxy/galaxy-dist/tools/iAssembler'; | |
| 64 | |
| 65 4. Add the Galaxy tool information to tool_conf.xml in /galaxy-dist/ | |
| 66 | |
| 67 5. Restart Galaxy using | |
| 68 | |
| 69 ./run.sh --stop-daemon | |
| 70 | |
| 71 and then | |
| 72 | |
| 73 ./run.sh --reload --daemon |