The National Cancer Institute’s Genomic Data Commons (GDC) produces a tool which facilitates data transfer to and from their data repository called gdc-client, which is open sourced on GitHub.
My first pass at building it gave an error while trying to build lxml without Cython:
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
The fix was to build and install lxml from source, using Cython. And Cython < 3 is needed, i.e. Cython 0.29.x.
Once lxml 4.4.2 was installed manually, following the gdc-client build instructions was successful, and the gdc-client script was created.
For more detail, see this Gist.
