GDC Data Transfer Tool for RHEL release 6?
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4.8 years ago
biomed_dev ▴ 10

I see the GDC provides binaries for ubuntu 14, but my group uses RHEL release 6. Anybody have experience in building the Data Transfer Tool from source using the code in GDC’s github repo? Thanks

gdc tcga RHEL • 2.8k views
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Have you tried running the binary on your RHEL instance? It's probably worth a shot.

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4.8 years ago
Ian0998 ▴ 10

Unfortunately running the binary for Ubuntu 14.04 in a CentOS6.x/RHEL6/SL6 environment will not work due to a glibc incompatibility. If you need to run the client in a CentOS6.x/RHEL6/SL6 environment the GDC is currently testing out a beta client. The client runs on the native python 2.6.x and glibc library. Here are the install instructions for the Beta release of the gdc-client (data transfer tool) v1.2.0 -

@@@ Start of Client Install Instructions @@@

  • Update system - Not Needed but a good idea.

    sudo yum update

  • Install git

    sudo yum install git

  • Clone the source for gdc-client

    git clone https://github.com/NCI-GDC/gdc-client/

  • Change into download

    cd gdc-client

  • Switch to the proper branch

    git checkout feat/python-26

    git pull origin feat/python-26

  • Install parcel dependencies

    sudo yum install -y python-devel python-setuptools gcc gcc-c++ libxml2-devel libxslt-devel libxml2-python

  • Install repository to install pip

    sudo rpm -ivh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm

  • Install pip and virtualenv

    sudo yum install -y python-pip python-virtualenv

  • If that fails, remove the epel-release package:

    sudo rpm -e epel-release-6-8.noarch

  • And then install the packages manually, downloading from here:

    wget http://dl.fedoraproject.org/pub/epel/6/x86_64/python-pip-7.1.0-1.el6.noarch.rpm

    wget http://dl.fedoraproject.org/pub/epel/6/x86_64/python-virtualenv-1.10.1-1.el6.noarch.rpm

    sudo rpm -ivh python-pip-7.1.0-1.el6.noarch.rpm python-virtualenv-1.10.1-1.el6.noarch.rpm

  • Change to gdc-client directory, create venv, and activate it

    virtualenv venv

    source venv/bin/activate

  • Upgrade pip

    pip install --upgrade pip

  • Install jsonschema and setuptools

    pip install --upgrade jsonschema setuptools

  • Install parcel

    pip install -r requirements.txt

  • Install gdc-client

    python setup.py install

  • Running the DTT

    You will have to run the following commands below to start

    the virtual environment. This has to happen once per session.

    cd gdc-client

    source venv/bin/activate

@@@End of Instructions@@@

If users have other recommendations for installation on other environments it will be helpful to share those experiences to benefit other users here. For follow up assistance from GDC User Services please email the GDC Helpdesk at support@nci-gdc.datacommons.io. We will not necessarily respond to BioStars posts.

Ian

GDC User Support Services

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4.3 years ago
sandybioteck ▴ 20

I successfully installed the gdc-client on centos after the step "python setup.py install" as given in this post but still getting this error

(venvgdc) ss7mh@udc-ba35-37 /nv/vol80/hlilab/sandeep/software/gdc-client/gdc-client-develop $ gdc-client -h Traceback (most recent call last): File "/nv/vol80/hlilab/sandeep/software/gdc-client/venvgdc/bin/gdc-client", line 4, in <module> __import__('pkg_resources').run_script('gdc-client==1.2.0', 'gdc-client') File "/nv/vol80/hlilab/sandeep/software/gdc-client/venvgdc/lib/python2.7/site-packages/pkg_resources/__init__.py", line 745, in run_script self.require(requires)[0].run_script(script_name, ns) File "/nv/vol80/hlilab/sandeep/software/gdc-client/venvgdc/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1677, in run_script exec(script_code, namespace, namespace) File "/nv/vol80/hlilab/sandeep/software/gdc-client/venvgdc/lib/python2.7/site-packages/gdc_client-1.2.0-py2.7.egg/EGG-INFO/scripts/gdc-client", line 7, in <module>

File "build/bdist.linux-x86_64/egg/gdc_client/download/__init__.py", line 1, in <module> File "build/bdist.linux-x86_64/egg/gdc_client/download/parser.py", line 13, in <module> File "build/bdist.linux-x86_64/egg/gdc_client/download/client.py", line 8, in <module> ImportError: No module named download_stream

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