This page was last updated on Saturday, 12-Nov-2016 12:33:49 CST

Installation notes for SRA Toolkit version 2.3.5-2

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Prerequisites

1. $ sudo apt-get install libxml2-dev

Installation of compiled binaries

1. $ ver="2.8.0"
2. $ cd /programinstallers/
3. $ wget -N https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/$ver/sratoolkit.${ver}-ubuntu64.tar.gz
4. $ cd /usr/local/bin/
5. $ tar -zxvf /programinstallers/sratoolkit.${ver}-ubuntu64.tar.gz
6. Make a version-independent symlink
   $ ln -s sratoolkit.${ver}-ubuntu64 sratoolkit
7. Add to default PATH for all users
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/sratoolkit/bin"
   …

Installation from source code

These instructions are for installation from source code

1. $ ver="2.3.5-2"
2. Prepare installation directory
   $ sradir="/usr/local/bin/sra"
3. $ sralib="/usr/local/bin/sra/lib64"
4. $ mkdir /usr/local/bin/sra
5. Download and uncompress
   $ cd /programinstallers/
6. $ wget -N http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/$ver/sra_sdk-$ver.tar.gz
7. $ tar -zxvf sra_sdk-$ver.tar.gz
8. Compile
   $ cd sra_sdk-$ver
9. $ make help

   Before initial build, run 'make OUTDIR=<dir> out' from
   the project root to set the output directory of your builds.
   
   To select a compiler, run 'make <comp>' where
   comp = { GCC VC++ CLANG }.
   
   For hosts that support cross-compilation ( only Macintosh today ),
   you can run 'make <arch>' where arch = { i386 x86_64 sparc32 sparc64 }.
   
   To set a build configuration, run 'make <config>' where
   config = { debug profile release static dynamic }.

10. $ make OUTDIR="$sradir" out

      current build is linux static rel x86_64 build using gcc tools
      output target directory is '/usr/local/bin/sra/linux/gcc/stat/x86_64/rel'
    

11. $ make GCC

      current build is linux dynamic rel x86_64 build using gcc tools
      output target directory is '/usr/local/bin/sra/linux/gcc/dyn/x86_64/rel'
    

12. $ make dynamic

      current build is linux dynamic rel x86_64 build using gcc tools
      output target directory is '/usr/local/bin/sra/linux/gcc/dyn/x86_64/rel'
    

13. $ make
14. Add to default PATH
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/sra/bin64"
    …
    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/bin/sra/lib64"
    …
    export PATH LD_LIBRARY_PATH
15. Test
    $ sff-dump
    

    Usage:
      sff-dump [options]  [...]
      sff-dump [options] 
    
    Use option --help for more information
    
    sff-dump : 2.3.5
    
    

16. Cleanup
    $ cd /programinstallers ; rm sra_sdk-$ver -rf