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cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)

Home Page:http://cancerit.github.io/alleleCount/

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installation error

mheskett opened this issue · comments

commented

! Configure failed for Bio-DB-HTS-2.9. See /home/users/heskett/.cpanm/work/1515532118.89002/build.log for details. ! Installing the dependencies failed: Module 'Bio::DB::HTS' is not installed ! Bailing out the installation for alleleCount-v3.3.1.

linux 3.10.0-514.16.1.el7.x86_64

the build log says the same--> biodbhts is not installed. But isn't this included?

thanks!

commented

Hi @mheskett , please could you provide the following information:

  1. Operating system (I think RedHat from the above string)
  2. Attach the full output of setup.sh by redirecting stdout+stderr to file

This looks like htslib has failed to build rather than the perl-lib.

Thanks

commented

Just read your previous issue that you closed where autodie was not found. This would suggest you were attempting to install with perl <5.10.1 (~2007 release, 7 years prior to this repository being created) as it has been a core library since then.

If you've resumed an install after changing to point to a newer perl you will need to start the build process from a clean checkout/archive, or delete the install_tmp folder before running ./setup.sh <install_loc>

commented

build.log

CentOS Linux release 7.3.1611 (Core)
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

CentOS Linux release 7.3.1611 (Core)
CentOS Linux release 7.3.1611 (Core)

commented

Please can you provide the command you used to invoke this build? The log you have provided suggests that you have run the perl Makefile rather than setup.sh <INSTALL TO> as there should be install steps for the C libraries performed separately to the perl modules.

commented

I've just run a build on a clean image of CentOS 7:

$ hostnamectl
   Static hostname: centos.localdomain
Transient hostname: centos
         Icon name: computer-vm
           Chassis: vm
        Machine ID: 56d65f493d8f854534fe792ecf014b83
           Boot ID: 3b491dbb00164441b630e9aab9971206
    Virtualization: kvm
  Operating System: CentOS Linux 7 (Core)
       CPE OS Name: cpe:/o:centos:centos:7
            Kernel: Linux 3.10.0-327.28.3.el7.x86_64
      Architecture: x86-64

I had to add some packages but it does build fine. Below is my history, I've deleted commands where I was trying to find relevant packages.

Unfortunately RedHat/CentOS are known for removing thing from the core perl release which confuses matter.

    5  sudo yum install bzip2
    6  sudo yum install autoconf automake gcc libtool make pkgconfig zlib-devel libcurl-devel
    7  sudo yum install autoconf zlib-devel libcurl-devel openssl-devel ncurses-devel 
    8  sudo yum install perl perl-devel perl-Test-Simple perl-libwww-perl perl-autodie
    9  curl -sSL https://github.com/cancerit/alleleCount/archive/v3.3.1.tar.gz | tar zx
   10  cd alleleCount-3.3.1/
   11  ./setup.sh ~/local
   12  history

Can you try this please?

commented

Thanks for the help! Tried again and I think there is success, here is the only error:

[fai_load] build FASTA index. [fai_load] build FASTA index. ./src/alleleCounter.c: In function ‘main’: ./src/alleleCounter.c:386:7: warning: unused variable ‘line’ [-Wunused-variable] char line[512]; ^ tests/bam_access_tests.c: In function ‘test_bam_access_get_position_base_counts’: tests/bam_access_tests.c:43:6: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] int res = bam_access_get_position_base_counts(chr,pos,stats);

I noticed that your readme doesn't document usage. How do I use aC?

commented

That's just a warning that a return value is not checked, quite common.

Provided you've installed to a location on your path (or added to your path)

alleleCounter --help

If not on path:

<install_loc>/bin/alleleCounter --help

I'll get that added to the current feature were working on (which removes most of the perl dependencies to simplify install).