Install bam-readcount

Question

[Chris]

Hello bioinformaticians,

I run this code to install bam-readcount:

 cd $RNA_HOME/student_tools/   
export SAMTOOLS_ROOT=$RNA_HOME/student_tools/samtools-1.9   
git clone https://github.com/genome/bam-readcount.git   
cd bam-readcount   
cmake -Wno-dev $RNA_HOME/student_tools/bam-readcount   
make

After a quite long-running, I got error:

[ 11%] Built target boost-1.55 [ 11%] Built target __bc_predepends [ 22%] Built target bzip2 [ 33%] Built target mbedtls [ 34%] Performing build step for 'curl' Making all in lib CCLD libcurl.la /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_ciphersuites.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_tls.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(debug.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_cli.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_srv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object;

Would you please tell me how to fix this? Thank you so much!

[Pierre Lindenbaum]

you should use conda to install this: https://anaconda.org/bioconda/bam-readcount

[Chris]

Thank you for your suggestion! I run the code on a Linux server and when I type conda, it got the error conda command not found.

[Pierre Lindenbaum]

it got the error conda command not found.

https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links

[Chris]

Thank you for your help! So I should contact the server manager, right? I am quite confused quick one I should install.