Differences

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--- augustus-software [2016/02/17 05:50] – created joguya
+++ augustus-software [2018/01/07 15:40] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 3.2.1
+  * Version: 3.3
-  * Added: February, 2016
+  * Added: January, 2018
   * Link: http://bioinf.uni-greifswald.de/augustus/
@@ Line 14: / Line 14: @@
 </code>
-Load augustus
+Load one version into your environment:
-<code>$ module load augustus/3.2.1</code>
+<code>$ module load augustus/3.3</code>
 ===== Installation ======
@@ Line 21: / Line 21: @@
 <code>$ cd /tmp
-$ cd /tmp
+$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz
-$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.1.tar.gz
+$ tar xf augustus-3.3.tar.gz
-$ tar -xvf augustus-3.2.1.tar.gz
+$ cd augustus
-$ cd augustus-3.2.1
+$ sed -i 's/#ZIPINPUT = true/ZIPINPUT = true/' common.mk
-$ sed -i 's/^#ZIPINPUT/ZIPINPUT/g' common.mk
+$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/bamtools/2.5.1/lib64 LDFLAGS="$LDFLAGS -L/export/apps/bamtools/2.5.1/lib64" CFLAGS="$CFLAGS -I/export/apps/bamtools/2.5.1/include/bamtools"
-$ cd src
+$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.5.1/include/bamtools#' auxprogs/bam2hints/Makefile
+$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.5.1/include/bamtools#' auxprogs/filterBam/src/Makefile
+$ sudo yum install boost-devel
+$ make clean
 $ make
-$ cd ../
+$ sudo mkdir /export/apps/augustus/3.3
-$ sudo mkdir -p /export/apps/augustus/3.2.1/
+$ sudo chown aorth /export/apps/augustus/3.3
-$ sudo cp -r . /export/apps/augustus/3.2.1/
+$ make INSTALLDIR=/export/apps/augustus/3.3 install
-</code>
+$ find /export/apps/augustus/3.3 -type d -exec chmod 755 {} \;
+$ find /export/apps/augustus/3.3/config/ -type f -exec chmod 644 {} \;
+$ find /export/apps/augustus/3.3/scripts -type f -exec chmod 644 {} \;
+$ find /export/apps/augustus/3.3/scripts -iname '*.pl' -exec chmod 755 {} \;
+$ sudo chown -R root:root /export/apps/augustus/3.3</code>
+Augustus requires bamtools at compile time (but not during run time).