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fraggenescan-software [2015/07/06 12:38]
joguya created
fraggenescan-software [2020/03/15 12:17] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 1.19+  * Version: 1.30
   * Added: July, 2015   * Added: July, 2015
-  * Updated: ​July2015 +  * Updated: ​March2020 
-  * Link: http://​omics.informatics.indiana.edu/​FragGeneScan/​+  * Link: https://​omics.informatics.indiana.edu/​FragGeneScan/​
  
 ===== Usage ===== ===== Usage =====
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 See versions of FragGeneScan which are available: See versions of FragGeneScan which are available:
 <​code>​$ module avail fraggenescan</​code>​ <​code>​$ module avail fraggenescan</​code>​
 +
 +Load one version into your environment and run it:
 +
 +<​code>​$ module load fraggenescan/​1.30
 +$ run_FragGeneScan.pl -genome=[seq_file_name] -out=[output_file_name] -complete=[1 or 0] -train=[train_file_name] -thread=[num_thread]</​code>​
 +
 +**Note:** Please remember to specify the same number of CPU threads as you have requested in your SBATCH job parameters.
  
 ===== Installation ====== ===== Installation ======
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 <​code>​ <​code>​
-wget "http://​downloads.sourceforge.net/​project/​fraggenescan/​FragGeneScan1.19.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Ffraggenescan%2F&ts=1436173470&​use_mirror=liquidtelecom" ​-O "FragGeneScan1.19.tar.gz" +$ cd /tmp 
-tar -xvf FragGeneScan1.19.tar.gz +wget 'https://​downloads.sourceforge.net/​project/​fraggenescan/​FragGeneScan1.30.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Ffraggenescan%2Ffiles%2FFragGeneScan1.30.tar.gz%2Fdownload&ts=1584261823' ​-O FragGeneScan1.30.tar.gz 
-cd FragGeneScan1.19 +tar xf FragGeneScan1.30.tar.gz  
-scl enable devtoolset-bash +cd FragGeneScan1.30 
-make +scl enable devtoolset-bash 
-make fgs +make clean 
-sudo mkdir -p /​export/​apps/​fraggenescan/​1.19 +make fgs 
-find -perm /u+x -print -exec chmod  755 '​{}'​ \; +sudo mkdir -p /​export/​apps/​fraggenescan/​1.30 
-sudo cp -r . /​export/​apps/​fraggenescan/​1.19/+$ chmod 644 example/* train/* *.h *.c 
 +sudo cp -r . /​export/​apps/​fraggenescan/​1.30
 </​code>​ </​code>​
- 
fraggenescan-software.1436175512.txt.gz · Last modified: 2015/07/06 12:38 by joguya