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galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.
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Kraken installation via tool shed on Mac OSX 10.10.5 (for development) #315

Open carlfeberhard opened 8 years ago

carlfeberhard commented 8 years ago

I get the following error installing the 'kraken' part of the devteam kraken tool from the tool shed:

In file included from krakendb.cpp:20:
./kraken_headers.hpp:36:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^
1 error generated.
make: *** [krakendb.o] Error 1
/bin/sh: /bin/true: No such file or directory

tool: devteam kraken 0.10.5

bgruening commented 8 years ago

@carlfeberhard can this be because Clang does not yet support OpenMP and you are using Clang instead of GCC?

nekrut commented 8 years ago

Use my branch for kraken update

Anton Nekrutenko Professor of Biochemistry and Molecular Biology http://nekrut.bx.psu.edu http://nekrut.bx.psu.edu (814) 826-9628

On Mon, Dec 14, 2015 at 5:43 PM, carlfeberhard notifications@github.com wrote:

I get the following error installing the 'kraken' part of the devteam kraken tool from the tool shed:

In file included from krakendb.cpp:20: ./kraken_headers.hpp:36:10: fatal error: 'omp.h' file not found

include 

     ^

1 error generated. make: *\ [krakendb.o] Error 1 /bin/sh: /bin/true: No such file or directory

tool: devteam kraken 0.10.5

— Reply to this email directly or view it on GitHub https://github.com/galaxyproject/tools-devteam/issues/315.

nekrut commented 8 years ago

I'm sorry - I confused this with taxonomy. Yes this may be the problem bjorn has indicated

Anton Nekrutenko Professor of Biochemistry and Molecular Biology http://nekrut.bx.psu.edu http://nekrut.bx.psu.edu (814) 826-9628

On Tue, Dec 15, 2015 at 4:58 PM, Anton Nekrutenko anton@nekrut.org wrote:

Use my branch for kraken update

Anton Nekrutenko Professor of Biochemistry and Molecular Biology http://nekrut.bx.psu.edu http://nekrut.bx.psu.edu (814) 826-9628

On Mon, Dec 14, 2015 at 5:43 PM, carlfeberhard notifications@github.com wrote:

I get the following error installing the 'kraken' part of the devteam kraken tool from the tool shed:

In file included from krakendb.cpp:20: ./kraken_headers.hpp:36:10: fatal error: 'omp.h' file not found

include 

     ^

1 error generated. make: *\ [krakendb.o] Error 1 /bin/sh: /bin/true: No such file or directory

tool: devteam kraken 0.10.5

— Reply to this email directly or view it on GitHub https://github.com/galaxyproject/tools-devteam/issues/315.