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  • Install Fastx (zz)

    Fastx-toolkit installation on CentOS
    =====================================
    
    Tested on CentOS release 5.3 (FINAL) x86_64
    
    Prerequisites:
      pkg-config, gcc, g++, wget
     
    Using YUM, install gcc, g++, pkg-config and wget
    
     $ sudo yum install pkgconfig.x86_64 gcc.x86_64 gcc-c++.x86_64 wget.x86_64
     
    Verify GCC/G++ versions - must be atleast 4.1
    
     $ gcc -v
     Using built-in specs.
     Target: x86_64-redhat-linux
     Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
     Thread model: posix
     gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)
     
    
    Fastx-Toolkit Installation:
    
     //
     // Install libgtextutils
     //
     $ wget http://cancan.cshl.edu/labmembers/gordon/files/libgtextutils-0.6.tar.bz2
     $ tar -xjf libgtextutils-0.6.tar.bz2
     $ cd libgtextutils-0.6
     $ ./configure
     $ make
     $ sudo make install
     $ cd ..
     
     // Tell pkg-config to look for libraries in /usr/local/lib, too.
     $ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH  ##### This is very IMPORTANT!!!!!!!!!!!!
     //
     // Install fastx-toolkit
     //
     $ wget http://cancan.cshl.edu/labmembers/gordon/files/fastx_toolkit-0.0.12.tar.bz2 
     $ tar -xjf fastx_toolkit-0.0.12.tar.bz2 
     $ cd fastx_toolkit-0.0.12
     $ ./configure
     $ make
     $ sudo make install
     
    
    Sanity check:
    
     //
     // run fastx_uncollapser without full path,
     // should find the executable in /usr/local/bin and also
     // be able to find /usr/local/lib/libgtextutils-0.6.so
     $ fastx_uncollapser -h
     usage: fasta_uncollapser [-c N] [-h] [-v] [-i INFILE] [-o OUTFILE]
     Part of FASTX Toolkit 0.0.12 by A. Gordon (gordon@cshl.edu)
    
      [-h]         = This helpful help screen.
      [-v]         = verbose: print short summary of input/output counts
      [-c N]       = Assume input is a tabular file (not FASTA file),
    		 And the collapsed identifier (e.g. '1-1000') is on column N.
      [-i INFILE]  = FASTA/Tabular input file. default is STDIN.
      [-o OUTFILE] = FASTA/Tabular output file. default is STDOUT.
    

    Original Link  http://hannonlab.cshl.edu/fastx_toolkit/install_centos.txt

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  • 原文地址:https://www.cnblogs.com/foreverycc/p/3511593.html
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