VICUNA Compiling issue, NCBI Toolkit v12, 64bit Ubuntu 14.01 LTS

[Sean Brimer]

Hello Group,

I have read the documentation and the threads from other people who have had a similar issue however I have not been able to figure out a solution. I was not able to ge the NCBI Toolkit v7, however a previous thread said that the 12 was working so I am hoping that is not the issue. When I compile VICUNA using the make command from the documintation I recieve this error

sean@LEN320:/usr/local/src/VICUNA_v1.3/src$ make
/usr/bin/g++ -fopenmp -O3 -I/usr/local/include/ncbi-tools++ -L/usr/local/lib *.cpp -o ../bin/vicuna-omp-v1.0 -lpthread -lxalgoalignnw -ltables -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbir/local

/usr/bin/ld: cannot find -lxncbir/local
collect2: error: ld returned 1 exit status

I'm still learning linux however I feel I followed the directions correctly and installed the toolkit, export the path, and now I seem to be missing a library or I have missed a step. If anyone can help that would be much appreciated. I feel like I am missing something simple.

Thanks
Sean

[Sean Brimer]

Hi Group,

For whatever reason Xiao's reply didn't show up here he said to install the NCBI toolkit 7 and gave me the archive link, however I am still stuck because I am not able to compile the corelib I keep receiving the following error

make[5]: Leaving directory `/usr/local/src/ncbi_cxx--7_0_0/GCC480-DebugOptMTDLL64/build/corelib'
FAILED: src/corelib/Makefile.corelib.lib
make[4]: *** [all.nonusr] Error 2
make[4]: Leaving directory `/usr/local/src/ncbi_cxx--7_0_0/GCC480-DebugOptMTDLL64/build/corelib'
make[3]: *** [all.real] Error 2
make[3]: Leaving directory `/usr/local/src/ncbi_cxx--7_0_0/GCC480-DebugOptMTDLL64/build/corelib'
make[2]: *** [all_r.needs-reqs] Error 2
make[2]: Leaving directory `/usr/local/src/ncbi_cxx--7_0_0/GCC480-DebugOptMTDLL64/build/corelib'
make[1]: *** [all_r.real] Error 5
make[1]: Leaving directory `/usr/local/src/ncbi_cxx--7_0_0/GCC480-DebugOptMTDLL64/build'
make: *** [all_r.needs-reqs] Error 2

I feel pretty sure the issues is the highlighted region of code. If any of you had this issue for the install, how did you get around it?

[Dave La]

Hey Sean,

Did you ever find a resolution to this issue?  I am also having the same install trying to compile NCBI Toolkit 7.

Thanks.

[Sean Brimer]

Hi Dave, 

I'm so sorry for the late reply, in short I did not and moved on. There is a pre-compiled version in the files as well, but I had issue with it and we the project went in a different direction so I didn't get to play with it. They have developed a viral-ngs pipeline which you can find here: https://github.com/broadinstitute/viral-ngs 

I have not played with this either but it might be helpful. 

again I'm sorry for not responding earlier

Good Luck

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