Fastx-toolkit installation on Ubuntu
=====================================
Tested on Ubuntu Server 9.10 amd64
Prerequisites:
pkg-config, gcc, wget
Using APT, install gcc and pkg-config
$ sudo apt-get install gcc g++ pkg-config wget
Verify GCC/G++ versions - must be atleast 4.2
$ gcc -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.1-4ubuntu8' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu8)
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 ..
//
// 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
//
// To run the fastx programs, you'll need to tell ubuntu about
// about the new shared library in /usr/local/lib.
//
// Method one:
// add /usr/local/lib to LD_LIBRARY_PATH environment variable
$ export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
//
// Method two:
// run 'ldconfig' to update the shared libraries cache
$ sudo ldconfig
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.
=====================================
Tested on Ubuntu Server 9.10 amd64
Prerequisites:
pkg-config, gcc, wget
Using APT, install gcc and pkg-config
$ sudo apt-get install gcc g++ pkg-config wget
Verify GCC/G++ versions - must be atleast 4.2
$ gcc -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.1-4ubuntu8' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu8)
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 ..
//
// 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
//
// To run the fastx programs, you'll need to tell ubuntu about
// about the new shared library in /usr/local/lib.
//
// Method one:
// add /usr/local/lib to LD_LIBRARY_PATH environment variable
$ export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
//
// Method two:
// run 'ldconfig' to update the shared libraries cache
$ sudo ldconfig
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.