This page was last updated on Friday, 11-Nov-2016 11:46:37 CST

Installation notes for Celera Assembler development version, revision 4358 (compiled June 30, 2013)

Home Page

Prerequisites

svn
$ sudo apt-get install subversion

kmer, part of sim4db suite
the version required is newer than what is available from the web site
instructions are included in the install procedure shown below

Installation

1. $ cd /pacbio/
2. $ svn checkout svn://svn.code.sf.net/p/wgs-assembler/svn/trunk/src src
3. Change for PacBio support:
   $ nano src/AS_global.H
   change
   #define AS_READ_MAX_NORMAL_LEN_BITS 11
   to
   #define AS_READ_MAX_NORMAL_LEN_BITS 15
4. kmer installation
   1. Following is necessary to fix the error
      gmake[1]: *** No rule to make target `sweatShop.H', needed by `classifyMates.o'. Stop.
      http://sourceforge.net/p/wgs-assembler/bugs/236/
      $ wget -N http://www.kmer.sf.net/kmer1956.tar.bz2
   2. $ tar -jxvf kmer1956.tar.bz2
   3. $ mv kmer1956 kmer
   4. New method:
      $ svn checkout svn://svn.code.sf.net/p/kmer/code/trunk kmer-code (from http://sourceforge.net/p/kmer/code/HEAD/tree/)
   5. $ cd kmer-code
   6. $ ./configure.sh
   7. $ make
   8. $ make install
   9. $ cd ..
   10. Makefiles assume directory is called kmer, so simplest fix is to make a symlink
       $ ln -s kmer-code kmer
5. Make some changes to the AS_BAT Makefile:
   $ nano src/AS_BAT/Makefile
   change
   #INC_IMPORT_DIRS += $(KMER)/include
   INC_IMPORT_DIRS += $(LOCAL_WORK)/kmer-code/libutil
   #LIB_IMPORT_DIRS += $(KMER)/lib
   LIB_IMPORT_DIRS += $(LOCAL_WORK)/kmer-code/libutil
6. $ cd src
7. $ gmake ( or just make )
8. Compiled binaries are in /pacbio/Linux-amd64/bin/