Question: Installing blasr with make failed
0
gravatar for 1348988193
12 months ago by
13489881930
13489881930 wrote:

Hello,everyone!I have been working on this installation for the past several days.I installed blasr and LibBlasrConfig.h missing when make blasr.I found the same problem on github,but still can't solve it.Can anyone help me?

**$./configure.py --shared --sub --no-pbbam HDF5_INCLUDE=/home/cl/hdf5_fold/hdf5-1.8.16-linux-centos6-x86_64-gcc447-shared/include/ HDF5_LIB=/home/cl/hdf5_fold/hdf5-1.8.16-linux-centos6-x86_64-gcc447-shared/lib/**

`uname`
Linux
writing to '/home/cl/blasr/defines.mk':
"""
LIBPBDATA_LIB        ?= /home/cl/blasr/libcpp/pbdata
LIBBLASR_LIBFLAGS    ?= -lblasr
HDF5_LIB             ?= /home/cl/hdf5_fold/hdf5-1.8.16-linux-centos6-x86_64-gcc447-shared/lib/
DL_LIBFLAGS          ?= -ldl
HDF5_INC             ?= /home/cl/hdf5_fold/hdf5-1.8.16-linux-centos6-x86_64-gcc447-shared/include/
LIBPBDATA_INC        ?= /home/cl/blasr/libcpp/pbdata
LIBPBIHDF_LIBFLAGS   ?= -lpbihdf
LIBPBIHDF_INC        ?= /home/cl/blasr/libcpp/hdf
LIBBLASR_LIB         ?= /home/cl/blasr/libcpp/alignment
SHELL                ?= bash
RT_LIBFLAGS          ?= -lrt
HDF5_LIBFLAGS        ?= -lhdf5_cpp -lhdf5
LIBPBDATA_LIBFLAGS   ?= -lpbdata
ZLIB_LIBFLAGS        ?= -lz
LIBBLASR_INC         ?= /home/cl/blasr/libcpp/alignment
PTHREAD_LIBFLAGS     ?= -lpthread
NOPBBAM              ?= 1
LIBPBIHDF_LIB        ?= /home/cl/blasr/libcpp/hdf
"""
------------------------------------------
**$make blasr**

...
In file included from iblasr/BlasrMiscs.hpp:4:0,
from Blasr.cpp:3:
iblasr/BlasrHeaders.h:22:28: fatal error: LibBlasrConfig.h: No such file or directory
compilation terminated.
make: *** [Blasr.o] Error 1
blasr install • 483 views
ADD COMMENTlink modified 12 months ago by WouterDeCoster38k • written 12 months ago by 13489881930

Since no one seems to have taken ownership of the issue submitted on GitHub I suggest that you should contact PacBio tech support directly to see if they have a solution.

ADD REPLYlink written 12 months ago by genomax65k
4
gravatar for WouterDeCoster
12 months ago by
Belgium
WouterDeCoster38k wrote:

I have been struggling with BLASR for days as well. But using (bio)conda is painless.

conda install -c bioconda blasr

I absolutely recommend conda for all your bioinformatics software needs.

ADD COMMENTlink written 12 months ago by WouterDeCoster38k

Thank you very much for your help.I will take your recommendation and try again.

ADD REPLYlink written 12 months ago by 13489881930
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