Question: soapdenovo2 install on UBUNTU 18.04LTS
0
gravatar for choi.yisoo.hi
27 days ago by
choi.yisoo.hi0 wrote:

Hello, is there anyone who install soapdenovo2 on UBUNTU18.04?

I want to use this program, but I cannot make this source.

I downloaded it from both https://github.com/aquaskyline/SOAPdenovo2, https://sourceforge.net/projects/soapdenovo2/.

Then decompress file and make.

make[1]: Leaving directory '/home/yisoo/Downloads/SOAPdenovo2-src-r240/standardPregraph'

/usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_import.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(sam.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_pileup.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(faidx.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(knetfile.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(sam_header.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(bgzf.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(kstring.o): relocation R_X86_64_32 against .text' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(bam_aux.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: ./sparsePregraph/inc/libbam.a(razf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC standardPregraph/main.o: In functionmain': main.c:(.text.startup+0xfa): undefined reference to `call_pregraph_sparse' /usr/bin/ld: final link failed: Symbol needs debug section which does not exist collect2: error: ld returned 1 exit status Makefile:65: recipe for target 'SOAPdenovo-63mer' failed make: * [SOAPdenovo-63mer] Error 1

I always receive this error.

Do you have any idea to solve it?

Please help me.

ADD COMMENTlink modified 25 days ago by colindaven1.3k • written 27 days ago by choi.yisoo.hi0
0
gravatar for colindaven
25 days ago by
colindaven1.3k
Hannover Medical School
colindaven1.3k wrote:

Works well via conda

First install miniconda3

Then

conda install -c conda-forge -c defaults -c r -c bioconda soapdenovo2
ADD COMMENTlink written 25 days ago by colindaven1.3k
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