FusionMap, mono 설치

1. mono 설치
URL : http://www.mono-project.com/Main_Page
Download : http://download.mono-project.com/sources/mono/
$ mkdir src
$ cd src
$ wget http://download.mono-project.com/sources/mono/mono-2.11.4.tar.bz2
$ tar jxvfp mono-2.11.4.tar.bz2
$ cd mono-2.11.4
$ mkdir /home/isbyeon/Tools
$ ./configure --with-large-heap=yes  --prefix=/home/isbyeon/Tools/mono-2.11.4 && make && make install

 

2. FusionMap 설치 및 예제실행
URL : http://www.omicsoft.com/fusionmap
$ cd;cd Tools
$ wget http://www.omicsoft.com/fusionmap/Software/FusionMap_2012-12-08.zip
$ unzip FusionMap_2012-12-08.zip
$ cd FusionMap
$ cd TestDataset
$ file /home/isbyeon/Tools/FusionMap/bin/FusionMap.exe

/home/isbyeon/Tools/FusionMap/bin/FusionMap.exe: PE32 executable for MS Windows (console) Intel 80386 32-bit Mono/.Net assembly

 

$ vi secontrol_InputPairedEndReads-linux.config

<Files>
#/test/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_1.fastq
#/test/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_2.fastq
/home/isbyeon/Tools/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_1.fastq
/home/isbyeon/Tools/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_2.fastq

 

<Options>
PairedEnd=True
RnaMode=True
#Use32BitMode=False
Use32BitMode=True    ### FusionMap 32-bit이므로 True
ThreadNumber=8 //Possible values: 1-100. Default value=1
FileFormat=FASTQ // Possible values: FASTQ, QSEQ, FASTA. Default value=FASTQ
MinimalFusionAlignmentLength=25 //Possible values: 15-50. Default value=25 (alpha)
FusionReportCutoff=1 // Possible values: 1-1000. Default value=1 (beta)
NonCanonicalSpliceJunctionPenalty=4 //Possible values: 01-. Default value = 2 (G)
MinimalHit=2 // Minimal distinct read; Possible values: 1-10000, Default value =2
MinimalRescuedReadNumber=1 // Minimal rescued read number. Default value = 1
OutputFusionReads=True // Possible values: True, False. Default value = True
FilterBy=DefaultList //advanced filtering using default black list from FusionMap, set to None to avoid automatic downloading

 

<Output>
TempPath=/tmp
#OutputPath=/test/FusionMap/TestDataset/output
OutputPath=/home/isbyeon/Tools/FusionMap/TestDataset/output
OutputName=TestDataset_InputPEReads

$ /home/isbyeon/Tools/mono-2.11.4/bin/mono \

/home/isbyeon/Tools/FusionMap/bin/FusionMap.exe \

--semap \

/home/isbyeon/Tools/FusionMap \

Human.B37 \

RefGene \

/home/isbyeon/Tools/FusionMap/TestDataset/secontrol_InputPairedEndReads-linux.config

※ Use32BitMode=False시 아래와 같은 에러 발생

#/test/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_1.fastq||/home/isbyeon/Tools/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_1.fastq...Error occured in module::semap
Error=ApplicationName='mono', CommandLine='"/home/isbyeon/Tools/FusionMap/bin/oalign.exe" RnaSeqG_Fusion "#/test/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_1.fastq||/home/isbyeon/Tools/FusionMap/TestDataset/input/DatasetP2_SimulatedReads_1.fastq" "/tmp/2013.1.4.9da5bbb81b881e8/78c01488a033596c.51cb9ce71a983232.pi" "/tmp/2013.1.4.9da5bbb81b881e8/4e76b9063957008a.51cb9ce71a983232.errorlog"', CurrentDirectory='', Native error= Cannot find the specified file
StackTrace=  at System.Diagnostics.Process.Start_noshell (System.Diagnostics.ProcessStartInfo startInfo, System.Diagnostics.Process process) [0x00000] in <filename unknown>:0
  at System.Diagnostics.Process.Start_common (System.Diagnostics.ProcessStartInfo startInfo, System.Diagnostics.Process process) [0x00000] in <filename unknown>:0
  at System.Diagnostics.Process.Start () [0x00000] in <filename unknown>:0
  at (wrapper remoting-invoke-with-check) System.Diagnostics.Process:Start ()
  at Omicsoft.OProcess.Run (ILogger logger, Boolean throwIndividualErrors, System.String& errorMessage) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Alignment.OAlign.RunOneAlignAsProcess (ILogger logger, System.String mode, Omicsoft.PropertyItem pi, System.String fileOrPair, System.String& errorMessage) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Alignment.OAlign+<>c__DisplayClass4.<RunAlign>b__0 (Int32 cpuIndex, Omicsoft.JobContext jc) [0x00000] in <filename unknown>:0
  at Omicsoft.JobRunner.Run (ILogger logger, Omicsoft.Job job, Int32 cpuNumber) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Alignment.OAlign.RunAlign (ILogger logger, System.String mode, Omicsoft.PropertyItem pi, Omicsoft.StringVector files, Boolean spawnOff, Omicsoft.Data.TableData& alignmentSummary, Omicsoft.Data.TableData& errorReport) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Shell.NgsShell.MapFusionReads (ILogger logger, IProject project, Omicsoft.StringVector files, System.String refLibID, System.String geneModelID, IAttributeContainer attributes, IAttributes adapterAttributes, System.String outputName) [0x00000] in <filename unknown>:0
  at oshell.oshell.Main (System.String[] args) [0x00000] in <filename unknown>:0