[maker-devel] Problem with RMBlast installation

[Carson Holt]

You only need to add the directory location for executables you plan on
calling yourself from the command line.  You don't need to add RMBlast to
the PATH for example because you should never use it directly.  RepeatMasker
knows where it is once configured, and you want to use NCBI's BLAST.

Thanks,
Carson

From:  Daniel Fernández <daniel.fer.u at gmail.com>
Date:  Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Cc:  "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>,
Daniel Fernández <daniel.fer.u at gmail.com>
Subject:  Re: [maker-devel] Problem with RMBlast installation

Ok, I unpack this file, I have 3 directories (bin include lib) and the
readme file, you tell me add this to my $PATH, but I  add to my path all
executables (bin), but the other 2 directories? I don't think that I have to
add to my path, is different to Blast+, in blast+ I only copy the
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my
path, so I will have many duplicate executables, does this not cause a
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
> Hi Daniel -
> 
> Just download, unpackage the precompiled (
> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell
> RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is
> for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your
> pick.
> 
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fernández wrote:
> 
>> Hi,
>> 
>> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the
>> README file tell me that I need RMBlast, but I don't know what file I have to
>> choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or
>> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each
>> version the README file is the same, and there tell me how I can install it,
>> but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well,
>> when I try to install it, I type this
>> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast
>> --without-debug
>> This show me error, and I type make and this show stop.
>> 
>> Can you help me please?
>> 
>> This show me when I type $./configure --with-mt
>> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------------------
>> configure: loading site script ./src/build-system/config.site
>> configure: loading cache config.cache
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> 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 ANSI C... none needed
>> checking for g++... no
>> checking for c++... no
>> checking for gpp... no
>> checking for aCC... no
>> checking for CC... no
>> checking for cxx... no
>> checking for cc++... no
>> checking for cl... no
>> checking for FCC... no
>> checking for KCC... no
>> checking for RCC... no
>> checking for xlC_r... no
>> checking for xlC... no
>> checking whether we are using the GNU C++ compiler... no
>> checking whether g++ accepts -g... no
>> adjusted C   compiler: /usr/bin/gcc
>> ./src/build-system/configure: line 4404: type: g++: not found
>> dirname: missing operand
>> Try `dirname --help' for more information.
>> configure: error: Do not know how to build MT-safe with compiler g++
>> ./src/build-system/configure: line 4187: g++: command not found
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
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