Differences

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--- augustus-software [2017/05/23 15:02] – aorth
+++ augustus-software [2017/05/23 15:08] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 3.2.1
+  * Version: 3.2.3
-  * Added: February, 2016
+  * Added: May, 2017
   * Link: http://bioinf.uni-greifswald.de/augustus/
@@ Line 15: / Line 15: @@
 Load augustus
-<code>$ module load augustus/3.2.1</code>
+<code>$ module load augustus/3.2.3</code>
 ===== Installation ======
@@ Line 21: / Line 21: @@
 <code>$ cd /tmp
-$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.1.tar.gz
+$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz
-$ tar -xvf augustus-3.2.1.tar.gz
+$ tar xf augustus-3.2.3.tar.gz
-$ cd augustus-3.2.1
+$ cd augustus-3.2.3
-$ sed -i 's/^#ZIPINPUT/ZIPINPUT/g' common.mk
+$ sed -i 's/#ZIPINPUT = true/ZIPINPUT = true/' common.mk
-$ cd src
+$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/bamtools/2.4.0/lib LDFLAGS="$LDFLAGS -L/export/apps/bamtools/2.4.0/lib" CFLAGS="$CFLAGS -I/export/apps/bamtools/2.4.0/include"
-$ make
+$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.4.0/include#' auxprogs/bam2hints/Makefile
-$ cd ../
+$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.4.0/include#' auxprogs/filterBam/src/Makefile
-$ sudo mkdir -p /export/apps/augustus/3.2.1/
+$ sudo mkdir /export/apps/augustus/3.2.3
-$ sudo cp -r . /export/apps/augustus/3.2.1/
+$ sudo chown aorth /export/apps/augustus/3.2.3
+$ make INSTALLDIR=/export/apps/augustus/3.2.3 install
+$ sudo chown -R root:root /export/apps/augustus/3.2.3
 </code>
+Augustus requires bamtools, but for some reason it doesn't compile out of the box with the copy it comes with, so I told it to use the one already on our system.