Skip to content
This repository was archived by the owner on Aug 22, 2025. It is now read-only.
This repository was archived by the owner on Aug 22, 2025. It is now read-only.

Installation failure of bamliquidator on centos7 #82

@Yuxuan0060

Description

@Yuxuan0060

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!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions