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script launch xsqtools

Posted by jacob on Nov 4, 2011 12:31:52 PM

Follow this unofficial tutorial step by step to run xsq-tools on CentOS Linux 6 and OpenSuse Linux

 

1. If you are using CentOS Linux 6, OpenSuse Linux check which GNU LIBC version you have   installed. you can use this command

 

[jacob@localhost xsq-tools]$ ldd – -version
ldd (GNU libc) 2.12

Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

 

to run xsq-tools you will need GNU libc version 2.5+ !!

 

2. Get Official xsq-tools software package distribution from LifeTech/ABI

 

3. Open your favorite Linux console command and untar/unzip xsq-tools package.

 

4. If you want to convert your xsq solid 5500 output files you will need to use the convertFromXSQ.sh shell script.

 

5. Backup the official convertFromXSQ.sh shell script.

 

6. Download unofficial convertFromXSQ.sh shell script and save in your official xsq-tools directory,

 

7. Download script from here

 

8. Rename script convertFromXSQ.sh1.txt to convertFromXSQ.sh

 

9. Set execution permission to shell script ( chmod +x convertFromXSQ.sh )

 

10. Change to xsq-tools directory using linux command line (cd XSQ_Tools)

 

11. Extras: You can run unofficial convertFromXSQ.sh shell script like this samples

$ remember, cd XSQ-Tools first

 

(A) $ ./convertFromXSQ.sh -c data/Frag.xsq

 

(B, from any location)

$ convertFromXSQ.sh -c /home/jacob/XSQ-Tools/data/Frag.xsq -o $HOME

 

(C) $ ./convertFromXSQ.sh – -rootXSQ `pwd` -c data/Frag.xsq (- – rootXSQ paramater is useful to myXSQ application)

 

That’s all.

 

Notes:

[1] If you do not set XSQ_TOOLS environment variable, the  unofficial convertFromXSQ.sh set XSQ_TOOLS environment variable  automatically.

 

[2] Follow LifeTech/ABI official readme documentation to install xsq-tools, the   unofficial script updates your .bashrc ,bash_profile in user home   directories but I disabled exporting PATH environment variable because I   need to do some tests, if you want to run unofficial convertFromXSQ.sh from any   location you will need to update and export your PATH environment   variable manually.

 

I hope that help you , it works for me !!

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977 Views Tags: xsq, solid_5500, bioinformatics, qual


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