t-oginogin · April 20, 2014 12:14
diff --git a/file0.txt b/file0.txt
 OS：Ubuntu 12.04 LTS 64bit
diff --git a/file1.txt b/file1.txt
 VirtualBox-4.3.10
 vagrant_1.5.3
diff --git a/file10.txt b/file10.txt
 MYPATH=/usr/local/opt/ncbi_cxx/
 COMPILER=/usr/bin/g++
diff --git a/file11.txt b/file11.txt
 $ make
 $ cd ..
diff --git a/file12.txt b/file12.txt
 ~/research/VICUNA_v1.3/bin/vicuna-omp-v1.0
diff --git a/file13.txt b/file13.txt
 $ vi config/vicuna_config.txt
diff --git a/file14.txt b/file14.txt
 pFqDir /path_to_your_fastq_files_dir/
 //npFqDir /path_to_your_fastq_files_dir/
 //pFaDir /path_to_your_fasta_files_dir/
 //npFaDir /path_to_your_fasta_files_dir/

 outputDIR /path_to_your_output_dir/
diff --git a/file15.txt b/file15.txt
 $ cd ~/research/VICUNA_v1.3/
 $ OMP_NUM_THREADS=2 ./bin/vicuna-omp-v1.0 config/vicuna_config.txt
diff --git a/file16.txt b/file16.txt
 $ cd scripts/vicuna_analysis/
 $ make clean
 $ make all
 $ cd ../../
diff --git a/file17.txt b/file17.txt
 ~/research/VICUNA_v1.3/bin/vicuna_analysis
diff --git a/file18.txt b/file18.txt
 $ vi config/vanalysis_contig.txt
diff --git a/file19.txt b/file19.txt
 pFqDir /path_to_your_fastq_files_dir/
 //npFqDir /path_to_your_fastq_files_dir/
 //pFaDir /path_to_your_fasta_files_dir/
 //npFaDir /path_to_your_fasta_files_dir/

 trim_log_file /path_to_your_trim_log_file
 aln_file /path_to_your_aln_file

 outputDIR /path_to_your_analysis_output_dir/

 trim_log_fileとaln_fileはvicunaの出力結果のパスです。
diff --git a/file2.txt b/file2.txt
 $ sudo apt-get install python-software-properties
 $ sudo apt-get install software-properties-common
 $ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
 $ sudo apt-get update; sudo apt-get install gcc-4.7 g++-4.7
 $ sudo update-alternatives --remove-all gcc 
 $ sudo update-alternatives --remove-all g++
 $ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 20
 $ sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.7 20
 $ sudo update-alternatives --config gcc
 $ sudo update-alternatives --config g++
 $ sudo apt-get install make
diff --git a/file20.txt b/file20.txt
 $ ./bin/vicunAnalysis config/vanalysis config.txt
diff --git a/file21.txt b/file21.txt
 /Users/xxx/research/ncbi_tools++/12_0_0/ncbi_cxx--12_0_0/include/corelib/impl/ncbi_atomic_defs.h:96:12: fatal error: 'bits/c++config.h' file not found
diff --git a/file22.txt b/file22.txt
 $ sudo brew tap homebrew/versions
 $ sudo brew install gcc47
 $ export CC=/usr/local/bin/gcc-4.7
 $ export CXX=/usr/local/bin/g++-4.7
 $ export LD_LIBRARY_PATH=/usr/local/opt/gcc47/lib/gcc/x86_64-apple-darwin13.1.0/4.7.3/
 $ make
diff --git a/file23.txt b/file23.txt
 ld: symbol(s) not found for architecture x86_64
diff --git a/file24.txt b/file24.txt
 $ export CFLAGS="-lstdc++"
 $ export CXXFLAGS="-lstdc++"
diff --git a/file25.txt b/file25.txt
 /home/vagrant/research/ncbi_tools++/12_0_0/ncbi_cxx--12_0_0/GCC480-DebugOptMTDLL64/lib/libxobjread.so: undefined reference to `ncbi::objects::CPub_Base::DoSelect(ncbi::objects::CPub_Base::E_Choice, ncbi::CObjectMemoryPool*)'
diff --git a/file26.txt b/file26.txt
 ./configure --prefix=/usr/local/opt/ncbi_cxx --with-optimization --with-mt --with-dll
diff --git a/file27.txt b/file27.txt
 ./configure --prefix=/usr/local/opt/ncbi_cxx --with-optimization --with-mt
diff --git a/file28.txt b/file28.txt
 ./configure --prefix=/usr/local/opt/ncbi_cxx
diff --git a/file29.txt b/file29.txt
 $ wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA054/SRA054092/SRX154465/SRR513075.fastq.bz2
 $ wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA054/SRA054092/SRX154465/SRR513075_1.fastq.bz2
 $ wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA054/SRA054092/SRX154465/SRR513075_2.fastq.bz2
 $ bzip2 -d SRR513075.fastq.bz2
 $ bzip2 -d SRR513075_1.fastq.bz2
 $ bzip2 -d SRR513075_2.fastq.bz2
diff --git a/file3.txt b/file3.txt
 ~/research/VICUNA_v1.3
diff --git a/file4.txt b/file4.txt
 ~/research/VICUNA_v1.3/doc/vicuna.pdf
diff --git a/file5.txt b/file5.txt
 3 Quik Start - for external users
diff --git a/file6.txt b/file6.txt
 $ cd ~/research/ncbi_tools++/12_0_0/
 $ tar xvzf ncbi_cxx--12_0_0.tar.gz
diff --git a/file7.txt b/file7.txt
 $ cd ncbi_cxx--12_0_0
 $ ./configure --prefix=/usr/local/opt/ncbi_cxx --with-optimization --with-mt
 $ make
 $ sudo make install
diff --git a/file8.txt b/file8.txt
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/opt/ncbi_cxx/lib
diff --git a/file9.txt b/file9.txt
 $ cd ~/research/VICUNA_v1.3/src
 $ vi Makefile
	pFqDir /path_to_your_fastq_files_dir/
	//npFqDir /path_to_your_fastq_files_dir/
	//pFaDir /path_to_your_fasta_files_dir/
	//npFaDir /path_to_your_fasta_files_dir/

	outputDIR /path_to_your_output_dir/
	$ cd ~/research/VICUNA_v1.3/
	$ OMP_NUM_THREADS=2 ./bin/vicuna-omp-v1.0 config/vicuna_config.txt
	$ cd scripts/vicuna_analysis/
	$ make clean
	$ make all
	$ cd ../../
	$ sudo apt-get install python-software-properties
	$ sudo apt-get install software-properties-common
	$ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
	$ sudo apt-get update; sudo apt-get install gcc-4.7 g++-4.7
	$ sudo update-alternatives --remove-all gcc
	$ sudo update-alternatives --remove-all g++
	$ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 20
	$ sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.7 20
	$ sudo update-alternatives --config gcc
	$ sudo update-alternatives --config g++
	$ sudo apt-get install make
	$ sudo brew tap homebrew/versions
	$ sudo brew install gcc47
	$ export CC=/usr/local/bin/gcc-4.7
	$ export CXX=/usr/local/bin/g++-4.7
	$ export LD_LIBRARY_PATH=/usr/local/opt/gcc47/lib/gcc/x86_64-apple-darwin13.1.0/4.7.3/
	$ make
	$ wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA054/SRA054092/SRX154465/SRR513075.fastq.bz2
	$ wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA054/SRA054092/SRX154465/SRR513075_1.fastq.bz2
	$ wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA054/SRA054092/SRX154465/SRR513075_2.fastq.bz2
	$ bzip2 -d SRR513075.fastq.bz2
	$ bzip2 -d SRR513075_1.fastq.bz2
	$ bzip2 -d SRR513075_2.fastq.bz2
	$ cd ~/research/ncbi_tools++/12_0_0/
	$ tar xvzf ncbi_cxx--12_0_0.tar.gz
	$ cd ncbi_cxx--12_0_0
	$ ./configure --prefix=/usr/local/opt/ncbi_cxx --with-optimization --with-mt
	$ make
	$ sudo make install