Differences

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--- amos [2010/01/26 15:17] – created 172.26.0.166
+++ amos [2012/03/22 08:39] (current) – ikahugu
@@ Line 1: / Line 1: @@
-The AMOS source package has a name like: amos-1.4.5.tar.gz where 1.4.5 is the version of the code. Once you untar this file (using "tar -xzf amos-1.4.5.tar.gz" in Linux, or "gunzip -d amos-1.4.5.tar.gz | tar xf -" in other flavors of Unix) you will find the current AMOS distribution in a directory named amos-1.4.5. The next steps assume you have cd'd into this directory.
+==== AMOS ====
+The AMOS source package has a name like: amos-3.1.0.tar.gz where 3.1.0 is the version of the code. Once you untar this file (using "tar -xzf amos-3.1.0.tar.gz" in Linux, or "gunzip -d amos-3.1.0.tar.gz | tar xf -" in other flavors of Unix) you will find the current AMOS distribution in a directory named amos-3.1.0. The next steps assume you have cd'd into this directory.
 AMOS uses the GNU autoconf package to reduce cross-platform compatibility issues. Before compiling the code you will need to run the configure script that will probe your system for the locations of all software packages required by AMOS.
 By simply running:
-./configure
+<code>./configure</code>
-you will prepare AMOS to be installed in the directory hosting the source package. This is OK if you are just testing AMOS. We recommend, however, that you provide the configure script with a more permanent home for AMOS, e.g.:
+You may get warnings from nucmer, delta-filter, show-coords and Qt4 toolkit
-./configure --prefix=/usr/local
+<code>
-will ultimately lead the AMOS directory hierarchy to be installed underneath /usr/local/.
+-- AMOS Assembler 3.1.0 Configuration Results --
+  C compiler:          gcc -g -O2
+  C++ compiler:        g++ -g -O2
+  GCC version:         gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-52)
+  Host System type:    x86_64-unknown-linux-gnu
+  Install prefix:      /home/evilliers/Downloads/amos-3.1.0
+  Install eprefix:     ${prefix}
+  See config.h for further configuration information.
+  Email <amos-help@lists.sourceforge.net> with questions and bug reports.
+WARNING! nucmer was not found but is required to run AMOScmp and minimus2
+   install nucmer if planning on using these programs
+WARNING! delta-filter was not found but is required to run AMOScmp-shortReads-alignmentTrimmed
+   install delta-filter if planning on using AMOScmp-shortReads-alignmentTrimmed
+WARNING! show-coords was not found but is required to run minimus2
+   install show-coords if planning on using minimus2
+WARNING! Qt4 toolkit malfunctioning but is required to run AMOS GUIs
+   try compiling GUIs manually or reinstall Qt4 toolkit to build GUIs
+   see config.log for more information on what went wrong
+</code>
+nucmer, delta-filter, show-coords are found in MUMmer which is already installed in HPC
+Load it by running
+<code>load module MUMmer/latest</code>
+For Qt4, append location of Qt4 in the configure script
+<code> ./configure --with-qmake-qt4=/usr/lib64/qt4/bin/qmake --prefix=/export/apps/amos/3.1.0/</code>
 After running configure, make sure you check the messages left on your screen to make sure no errors occured. Errors during the configure step can lead to an incomplete build.
 To compile the code you need to simply run:
-make
+<code>make</code>
 followed by
-make install
+<code>make install</code>
+http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS_Getting_Started
+http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
+AMOS is installed on HPC.