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I am trying to install the bio-informatics tool called DIAMOND. Unfortunately I am experiencing problems during installation:

The Ubuntu version that I am using is: Ubuntu 14.04 LTS

I am following this manual: https://github.com/bbuchfink/diamond/blob/master/README.rst

First I executed the command:

wget http://github.com/bbuchfink/diamond/releases/download/v0.7.9/diamond-linux64.tar.gz

and

tar xzf diamond-linux64.tar.gz

I executed the command in the directory where I want to install the program. The files that I have now are :

  • diamond
  • diamond-linux64.tar.gz
  • README.rst

When I execute a test command from the manual I receive this error :

markschuurman@markschuurman-OptiPlex-7010:~/Desktop/Onderzoek_BioCentre/DIAMOND_BLAST$ diamond makedb --in nr.faa -d nr
No command 'diamond' found, did you mean:
 Command 'kdiamond' from package 'kdiamond' (universe)
diamond: command not found

After that I tried "Compiling from source", "Compiling using CMake" and "Installing using Homebrew/Linuxbrew without succes".

Command from the manual and errors:

$ wget http://github.com/bbuchfink/diamond/archive/v0.7.9.tar.gz

No error

$ tar xzf v0.7.9.tar.gz

No error

$ cd diamond-0.7.9/src

No error

markschuurman@markschuurman-OptiPlex-7010:~/Desktop/Onderzoek_BioCentre/DIAMOND_BLAST/diamond-0.7.9/src$ ./install-boost

/libboost_chrono.a
common.copy ../boost/lib/libboost_chrono.a
common.mkdir bin.v2/libs/iostreams/build/gcc-4.8/release/link-static
common.mkdir bin.v2/libs/iostreams/build/gcc-4.8/release/link-static/threading-multi
gcc.compile.c++ bin.v2/libs/iostreams/build/gcc-4.8/release/link-static/threading-multi/file_descriptor.o
gcc.compile.c++ bin.v2/libs/iostreams/build/gcc-4.8/release/link-static/threading-multi/mapped_file.o
gcc.compile.c++ bin.v2/libs/iostreams/build/gcc-4.8/release/link-static/threading-multi/bzip2.o
libs/iostreams/src/bzip2.cpp:20:56: fatal error: bzlib.h: No such file or directory
 #include "bzlib.h"  // Julian Seward's "bzip.h" header.
                                                        ^
compilation terminated.

......

common.copy ../boost/lib/libboost_thread.a
common.mkdir bin.v2/libs/timer/build/gcc-4.8/release/link-static
common.mkdir bin.v2/libs/timer/build/gcc-4.8/release/link-static/threading-multi
gcc.compile.c++ bin.v2/libs/timer/build/gcc-4.8/release/link-static/threading-multi/auto_timers_construction.o
gcc.compile.c++ bin.v2/libs/timer/build/gcc-4.8/release/link-static/threading-multi/cpu_timer.o
gcc.archive bin.v2/libs/timer/build/gcc-4.8/release/link-static/threading-multi/libboost_timer.a
common.copy ../boost/lib/libboost_timer.a
...failed updating 2 targets...
...skipped 6 targets...
...updated 11465 targets...

markschuurman@markschuurman-OptiPlex-7010:~/Desktop/Onderzoek_BioCentre/DIAMOND_BLAST/diamond-0.7.9/src$ make
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_encoding.o algo/blast/core/blast_encoding.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_stat.o algo/blast/core/blast_stat.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_filter.o algo/blast/core/blast_filter.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_util.o algo/blast/core/blast_util.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_message.o algo/blast/core/blast_message.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_erf.o algo/blast/core/ncbi_erf.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_options.o algo/blast/core/blast_options.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_math.o algo/blast/core/ncbi_math.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_program.o algo/blast/core/blast_program.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/ncbi_std.o algo/blast/core/ncbi_std.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_psi_priv.o algo/blast/core/blast_psi_priv.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/raw_scoremat.o algo/blast/core/raw_scoremat.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_query_info.o algo/blast/core/blast_query_info.c
gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_seg.o algo/blast/core/blast_seg.c
g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o main.o main.cpp
g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o basic/options.o basic/options.cpp
g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o util/tinythread.o util/tinythread.cpp
g++ -o ../bin/diamond algo/blast/core/blast_encoding.o algo/blast/core/blast_stat.o algo/blast/core/blast_filter.o algo/blast/core/blast_util.o algo/blast/core/blast_message.o algo/blast/core/ncbi_erf.o algo/blast/core/blast_options.o algo/blast/core/ncbi_math.o algo/blast/core/blast_program.o algo/blast/core/ncbi_std.o algo/blast/core/blast_psi_priv.o algo/blast/core/raw_scoremat.o algo/blast/core/blast_query_info.o algo/blast/core/blast_seg.o main.o basic/options.o util/tinythread.o boost/lib/libboost_thread.a boost/lib/libboost_system.a boost/lib/libboost_timer.a boost/lib/libboost_chrono.a boost/lib/libboost_iostreams.a boost/lib/libboost_program_options.a -lpthread -lz -lrt
g++: error: boost/lib/libboost_iostreams.a: No such file or directory
make: *** [diamond] Error 1

Trying to use CMake:

wget http://github.com/bbuchfink/diamond/archive/v0.7.9.tar.gz

No error

tar xzf v0.7.9.tar.gz

No error

cd diamond-0.7.9

No error

mkdir build

No error

markschuurman@markschuurman-OptiPlex-7010:~/Desktop/Onderzoek_BioCentre/DIAMOND_BLAST/diamond-0.7.9$ cmake .. # Use cmake -DCMAKE_INSTALL_PREFIX=... to install to a different prefix.

Here I don't understand which prefix I need

Installing using Homebrew/Linuxbrew:

markschuurman@markschuurman-OptiPlex-7010:~/Desktop/Onderzoek_BioCentre/DIAMOND_BLAST/diamond-0.7.9$ brew install homebrew/science/diamond
No command 'brew' found, did you mean:
 Command 'qbrew' from package 'qbrew' (universe)
 Command 'brec' from package 'bplay' (universe)
brew: command not found
2
  • 1
    I think your issue is that you needed to run ./diamond makedb --in nr.faa -d nr after extracting the archive with the tar command - note you need the ./ before it to run it from the current directory, and you will also likely need the nr.faa file in the same directory.
    – Wilf
    Apr 21, 2015 at 15:30
  • 1
    I agree with @Wilf: the issue in the first case is simply that the untarred executable is not on your PATH; in the second case, it is that your system is missing the prerequisite development packages (it built OK on my 14.04 machine): in the third case, the tarball doesn't appear to provide support for cmake (no CMakeLists.txt files) so that's just not going to work. Apr 21, 2015 at 15:43

1 Answer 1

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The solution was to put the executable diamond in the directory /usr/bin. After that, without further installation steps, the program works.

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