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Old 10-03-2016, 02:46 PM   #1
zillur
Senior Member
 
Location: Puerto Rico

Join Date: Sep 2014
Posts: 106
Default Abyss Installation problem

Hi there,
I was trying to installation in my linux workstation. I have downloaded the package from github and tried to follow these steps:
Code:
Compiling ABySS from GitHub
===========================

When installing ABySS from GitHub source the following tools are
required:

* [Autoconf](http://www.gnu.org/software/autoconf)
* [Automake](http://www.gnu.org/software/automake)

To generate the configure script and make files:

	./autogen.sh

See "Compiling ABySS from source" for further steps.

Compiling ABySS from source
===========================

To compile and install ABySS in `/usr/local`:

	./configure
	make
	sudo make install
Upto ./configure it was running perfectly.
Code:
[root@genomics abyss-master]# ./autogen.sh 
+ aclocal
+ autoconf
+ autoheader
+ automake -a
[root@genomics abyss-master]# ./configure 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for ranlib... ranlib
checking for ghc... no
checking for ghc-pkg... no
./configure: line 5219: : command not found
checking for pandoc... no
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for std::hash<int>... no
checking for std::tr1::hash<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking if compiler needs -Werror to reject unknown flags... no
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking how to run the C++ preprocessor... g++ -E
checking functional usability... yes
checking functional presence... yes
checking for functional... yes
checking tr1/functional usability... yes
checking tr1/functional presence... yes
checking for tr1/functional... yes
checking boost/functional/hash.hpp usability... yes
checking boost/functional/hash.hpp presence... yes
checking for boost/functional/hash.hpp... yes
checking boost/property_map/property_map.hpp usability... yes
checking boost/property_map/property_map.hpp presence... yes
checking for boost/property_map/property_map.hpp... yes
checking google/sparse_hash_map usability... no
checking google/sparse_hash_map presence... no
checking for google/sparse_hash_map... no
checking unordered_map usability... no
checking unordered_map presence... no
checking for unordered_map... no
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking unordered_set usability... no
checking unordered_set presence... no
checking for unordered_set... no
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking boost/unordered_set.hpp usability... yes
checking boost/unordered_set.hpp presence... yes
checking for boost/unordered_set.hpp... yes
checking sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for g++ option to support OpenMP... -fopenmp
configure: error: ABySS should be compiled with Google sparsehash to
	reduce memory usage. It may be downloaded here:
	https://code.google.com/p/sparsehash/

	If you do not wish to use sparsehash, specify --without-sparsehash.
But when I tried to make:

Code:
[root@genomics abyss-master]# make
make: *** No targets specified and no makefile found.  Stop.
[root@genomics abyss-master]#
Any help about these issues.

Thank you very much for your comments.

Best regards
Zillur
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Old 10-04-2016, 04:24 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077
Default

Did you try using --without-sparsehash as suggested by the message above? Perhaps without that a Makefile will not get created.
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Old 10-04-2016, 09:52 AM   #3
zillur
Senior Member
 
Location: Puerto Rico

Join Date: Sep 2014
Posts: 106
Default

Thank you very much. After adding this argument, it works perfectly now. Thanks again.

Best Regards
Zillur
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