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--- fraggenescan-software [2015/07/06 09:38] – created joguya
+++ fraggenescan-software [2020/03/15 09:17] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 1.19
+  * Version: 1.30
   * Added: July, 2015
-  * Updated: July, 2015
+  * Updated: March, 2020
-  * Link: http://omics.informatics.indiana.edu/FragGeneScan/
+  * Link: https://omics.informatics.indiana.edu/FragGeneScan/
 ===== Usage =====
@@ Line 13: / Line 13: @@
 See versions of FragGeneScan which are available:
 <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 ======
@@ Line 18: / Line 25: @@
 <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-2 bash
+$ cd FragGeneScan1.30
-make
+$ scl enable devtoolset-7 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>