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installation on MAC #53
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Hi @nbahlis , sorry for the delayed response. Did you try following these detailed build instructions, which includes build instructions of Mac OS? https://github.com/BradnerLab/pipeline/wiki/bamliquidator#check-list It looks like you either don't have samtools installed or it isn't configured properly so the linker can't find If this doesn't help, can you please type into your terminal Thanks |
thank you John for your reply. that’s what I get for brew info samtools: homebrew/science/samtools: stable 1.2 (bottled), HEAD thank you
|
Sorry I haven't built on a Mac in a while and I'm afraid that the makefile needs changes to work with the current version of samtools. Can you please try adding
to this:
Unfortunately I won't have access to a mac for a few days, so I can't test this myself. If you can hold on for a few more days, I will test building on the mac and update the makefile as necessary. |
Thank you John Adding -lhts seem to have solved the problem. I will do some more testing. Nizar
|
Hi Nizar, You should be all set then. You can run Regards, |
I'll update the make file in a few days so that nobody else runs into the same problem you had. |
thanks John for your help, I had to install tables. I think the the test.py was fine.Please see below, do I need bokeh /Users…….../pipeline/bamliquidator_internal/bamliquidatorbatch/normalize_plot_and_summarize.py:243: RuntimeWarning: invalid value encountered in true_divide .Ran 22 tests in 1.811s OK thanks again
|
Hi Nizar, Your test result indicates that all tests passed. bokeh is optional, and is used to create html graphs like this: http://jdimatteo.github.io/Meta-Analysis/chr20.html It is up to you whether or not you want to use the bokeh graphs to visually inspect the output directly, or whether you just need the .txt or .hdf5 bamliquidator output. Regards, |
Super, thanks again John for your help Nizar
|
Hello,
thank you for the wonderful tools you made!
I tried installing bamliquidator on MAC OS X10.10 but I kept getting the error below. Any advice would be deeply appreciated.
MacBook-Pro-2:bamliquidator_internal nizarjacquesbahlis$ make
g++ -std=c++0x -O3 -g -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c bamliquidator.m.cpp
g++ -std=c++0x -O3 -g -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -pthread -c bamliquidator.cpp
g++ -O3 -g -Wall -o bamliquidator bamliquidator.o bamliquidator.m.o -lbam -lz -lpthread
Undefined symbols for architecture x86_64:
"_bam_destroy1", referenced from:
_bam_fetch in libbam.a(bam.o)
_sampileup in libbam.a(sam.o)
"_bam_hdr_destroy", referenced from:
_samclose in libbam.a(sam.o)
"_bam_init1", referenced from:
_bam_fetch in libbam.a(bam.o)
_sampileup in libbam.a(sam.o)
"_bam_name2id", referenced from:
_bam_parse_region in libbam.a(bam_aux.o)
"_bam_plp_destroy", referenced from:
_bam_plbuf_destroy in libbam.a(bam_plbuf.o)
"_bam_plp_init", referenced from:
_bam_plbuf_init in libbam.a(bam_plbuf.o)
"_bam_plp_next", referenced from:
_bam_plbuf_push in libbam.a(bam_plbuf.o)
"_bam_plp_push", referenced from:
_bam_plbuf_push in libbam.a(bam_plbuf.o)
"_bam_plp_reset", referenced from:
_bam_plbuf_reset in libbam.a(bam_plbuf.o)
"_bam_read1", referenced from:
_bam_fetch in libbam.a(bam.o)
"_bgzf_mt", referenced from:
_samthreads in libbam.a(sam.o)
"_fai_build", referenced from:
_samfaipath in libbam.a(sam.o)
"_hts_close", referenced from:
_samclose in libbam.a(sam.o)
"_hts_get_format", referenced from:
_samthreads in libbam.a(sam.o)
_samopen in libbam.a(sam.o)
"_hts_idx_destroy", referenced from:
liquidate(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, unsigned int, unsigned int, char, unsigned int, unsigned int) in bamliquidator.o
"_hts_idx_load", referenced from:
liquidate(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, unsigned int, unsigned int, char, unsigned int, unsigned int) in bamliquidator.o
"_hts_itr_destroy", referenced from:
_bam_fetch in libbam.a(bam.o)
"_hts_itr_next", referenced from:
_bam_fetch in libbam.a(bam.o)
"_hts_open", referenced from:
_samopen in libbam.a(sam.o)
"_hts_parse_reg", referenced from:
_bam_parse_region in libbam.a(bam_aux.o)
"_hts_set_fai_filename", referenced from:
_samopen in libbam.a(sam.o)
"_hts_verbose", referenced from:
_samopen in libbam.a(sam.o)
_samfaipath in libbam.a(sam.o)
"_sam_format1", referenced from:
_bam_format1 in libbam.a(bam.o)
_bam_view1 in libbam.a(bam.o)
"_sam_hdr_read", referenced from:
_samopen in libbam.a(sam.o)
"_sam_hdr_write", referenced from:
_samopen in libbam.a(sam.o)
"_sam_itr_queryi", referenced from:
_bam_fetch in libbam.a(bam.o)
"_sam_read1", referenced from:
_sampileup in libbam.a(sam.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [bamliquidator] Error 1
The text was updated successfully, but these errors were encountered: