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augustus-software [2017/05/23 15:08]
aorth
augustus-software [2018/01/07 15:40] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.2.3 +  * Version: 3.3 
-  * Added: May2017+  * Added: January2018
   * Link: http://bioinf.uni-greifswald.de/augustus/   * Link: http://bioinf.uni-greifswald.de/augustus/
  
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 </code> </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 ====== ===== Installation ======
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 <code>$ cd /tmp <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 $ 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'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).
augustus-software.1495552120.txt.gz · Last modified: 2017/05/23 15:08 by aorth