How to install gdc-client in Ubnutu

Question

[pxf109]

The instruction from the website, it is too confuse for me. I really hope someone can help me. Thank you.

[SES]

There is no way we can help without knowing what website you are referring to and what the error is.

[SES]

The point of this comment was to encourage OP to provide a minimum of details so we are not reduced to doing web searches for people. Obviously we can all do that, but the idea is to help with the issue and knowing what that is will save everyone a lot of time. It will also focus the answers and promote higher quality discussions.

Answer 1

[GenoMax]

Following should be all you need

https://gdc.cancer.gov/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip
unzip gdc-client_v1.6.1_Ubuntu_x64.zip
./gdc-client (to verify that program works)

Next step is optional. You could copy the client to a directory in your $PATH or to the location below (if it exists on your computer)

cp -pi ./gdc-client /usr/local/bin (if this does not work)
sudo cp -pi ./gdc-client /usr/local/bin

Edited (03/24/2022) to include link for the latest client.

Answer 2

[mbk0asis]

Check this site!

https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool

Answer 3

[neelablore]

Check this link

Installgdc

Answer 4

[Vanish007]

Genomax2 gave a good answer

I don't quite know where your error is, but check and make sure you are also in the correct operating system. If you are not in fact using Ubuntu and have Linux, you might have to build the client from the source code (download the source code from the GitHub website: https://github.com/NCI-GDC/gdc-client) and then build with Python.

Answer 5

[Ömer An]

conda install -c bioconda gdc-client

Answer 6

[prehensilecode]

Following the gdc-client build instructions may give an error in building lxml, one of the requirements. I have some instructions on how to work around that issue to successfully build gdc-client:

HOWTO build NCI-GDC/gdc_client

Notes on building https://github.com/NCI-GDC/gdc-client

Issue

Following their instructions, get error in building lxml Python package:

Building wheels for collected packages: lxml
  Building wheel for lxml (setup.py): started
  Building wheel for lxml (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [97 lines of output]
      Building lxml version 4.4.2.
      /tmp/pip-install-f3lu9_f_/lxml_2b73c7f2ec5345da925d4c9a21d250a8/setup.py:64: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.i
o/en/latest/pkg_resources.html
        import pkg_resources
      Building without Cython.
      Using build configuration of libxslt 1.1.34
      running bdist_wheel
      running build
      running build_py
      ...
       running build_ext
      building 'lxml.etree' extension
      creating build/temp.linux-x86_64-cpython-311
      creating build/temp.linux-x86_64-cpython-311/src
      creating build/temp.linux-x86_64-cpython-311/src/lxml
      gcc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DCYTHON_CLINE_IN_TRACEBACK=0 -I/usr/include/libxml2 -Isrc -Isrc/lxml/includes -I/home/chind/Src/gdc-client/venv/include -I/home/chind/opt/include/python3.11 -c src/lxml/etree.c -o build/temp.linux-x86_64-cpython-311/src/lxml/etree.o -w
      src/lxml/etree.c:289:12: fatal error: longintrepr.h: No such file or directory
        289 |   #include "longintrepr.h"
            |            ^~~~~~~~~~~~~~~
      compilation terminated.
      Compile failed: command '/usr/bin/gcc' failed with exit code 1
      creating tmp
      cc -I/usr/include/libxml2 -I/usr/include/libxml2 -c /tmp/xmlXPathInitymh_uec5.c -o tmp/xmlXPathInitymh_uec5.o
      cc tmp/xmlXPathInitymh_uec5.o -lxml2 -o a.out
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for lxml
  Running setup.py clean for lxml
Failed to build lxml
ERROR: Could not build wheels for lxml, which is required to install pyproject.toml-based projects

The key bit is Building without Cython. We can fix the error by using Cython instead of avoiding it.

Source directory

Assume gdc_client source code has been cloned to SOMEWHERE/gdc_client

Adding Cython < 3 to requirements.txt does not work

Manually adding Cython < 3 to setup.py and then running pip-compile to generate a new requirements.txt did not work: the same error occurs.

Manually installing Cython < 3 and lxml == 4.4.2

I found that manually installing Cython < 3 with pip, and installing lxml == 4.4.2 manually from source worked.

Do everything below while in the venv as per gdc_client build instructions.

• pip install "Cython<3"
• Download lxml 4.4.2 from https://github.com/lxml/lxml/releases/tag/lxml-4.4.2
  • tar xf lxml-4.4.2.tar.gz
  • cd lxml-4.4.2
  • python setup.py bdist_wheel
  • cd dist
  • pip install ./lxml-4.4.2-cp311-cp311-linux_x86_64.whl

Build gdc_client following standard instructions

• cd SOMEWHERE/gdc_client
• pip install -r requirements.txt
• python setup.py install

This creates the gdc_client executable script in SOMEWHRE/gdc_client/bin

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