Differences

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--- augustus-software [2017/05/23 15:08] – aorth
+++ augustus-software [2018/01/07 15:40] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 3.2.3
+  * Version: 3.3
-  * Added: May, 2017
+  * 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/3.2.3</code>
+<code>$ module load augustus/3.3</code>
 ===== Installation ======
@@ Line 21: / Line 21: @@
 <code>$ cd /tmp
-$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz
+$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz
-$ tar xf augustus-3.2.3.tar.gz
+$ tar xf augustus-3.3.tar.gz
-$ cd augustus-3.2.3
+$ cd augustus
 $ sed -i 's/#ZIPINPUT = true/ZIPINPUT = true/' common.mk
-$ 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="$CFLAGS -I/export/apps/bamtools/2.4.0/include"
+$ 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="$CFLAGS -I/export/apps/bamtools/2.5.1/include/bamtools"
-$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.4.0/include#' auxprogs/bam2hints/Makefile
+$ 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/2.4.0/include#' auxprogs/filterBam/src/Makefile
+$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.5.1/include/bamtools#' auxprogs/filterBam/src/Makefile
-$ sudo mkdir /export/apps/augustus/3.2.3
+$ sudo yum install boost-devel
-$ sudo chown aorth /export/apps/augustus/3.2.3
+$ make clean
-$ make INSTALLDIR=/export/apps/augustus/3.2.3 install
+$ make
-$ sudo chown -R root:root /export/apps/augustus/3.2.3
+$ sudo mkdir /export/apps/augustus/3.3
-</code>
+$ sudo chown aorth /export/apps/augustus/3.3
+$ make INSTALLDIR=/export/apps/augustus/3.3 install
+$ 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, 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.
+Augustus requires bamtools at compile time (but not during run time).