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Installation failure of bamliquidator on centos7 #82

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Yuxuan0060 opened this issue Sep 23, 2022 · 0 comments
Open

Installation failure of bamliquidator on centos7 #82

Yuxuan0060 opened this issue Sep 23, 2022 · 0 comments

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@Yuxuan0060
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Hi,

I tried to install bamliquidator on centos7. I ran the following commands first

sudo yum install wget
wget https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo rpm -ivh epel-release-latest-7.noarch.rpm
sudo yum install git make automake gcc gcc-c++ samtools-devel python-devel boost-devel hdf5-devel gperftools-devel tbb-devel zlib-devel lapack-devel samtools cmake
sudo easy_install-2.7 pip
install the python packages in a virtualenv or globally, e.g. sudo pip install bokeh==0.9.3 "openpyxl>=1.6.1,<2.0.0" tables unittest2 scipy

And then tried
git clone https://github.com/BradnerLab/pipeline.git
cd pipeline/bamliquidator_internal
make

But I got the following error messages:
g++ -O3 -g -Wall -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o bamliquidator bamliquidator.o bamliquidator.m.o -lbam -lz -lpthread
/usr/bin/ld: cannot find -lbam
collect2: error: ld returned 1 exit status
make: *** [bamliquidator] Error 1

Is there any idea how I can fix those errors and get bamliquidator installed on centos7? Thank you!

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