sequences/stream does not build

[ptrebert]

Hi,
for v2.1.1-alpha, the install process pip install . fails with the following error:

/VerityMap/veritymap/src/tools/sequences/stream.hpp:33:10: fatal error: zlib.h: No such file or directory
         33 | #include <zlib.h>
            |          ^~~~~~~~

However, cmake finds zlib in the environment

      -- Detecting CXX compile features - done
      -- Found Git: /usr/bin/git (found version "2.25.1")
      -- Found ZLIB: /tmp/env/venv/lib/libz.so (found version "1.2.11")
      -- Configuring done

$ pkg-config --libs --cflags zlib
-I/tmp/env/venv/include -L/tmp/env/venv/lib -lz

Any advice on how to fix that?

Best,
Peter

[seryrzu]

Hi Peter,

Can you please try the following command on a clean repository? From the root

python ./veritymap/main.py --reads veritymap/test_dataset/test_query.fasta veritymap/test_dataset/test_target.fasta -o test_launch

Does this work? It should say

Compiling mapper...
Mapper is compiled successful!

on the first run and then finish with VerityMap finished!.

If this works, please try

python3 setup.py install --record files.txt
veritymap --reads veritymap/test_dataset/test_query.fasta veritymap/test_dataset/test_target.fasta -o test_launch

does it end with
VerityMap finished!?

If this works, please use VerityMap this way.

To remove the package later, please do

xargs rm -rf < files.txt

I plan to add conda support at some point in the future.

[ptrebert]

thanks for the input - as shared via slack, I will get back to this problem asap

[baozg]

Will VerityMap include conda or singulariy support very soon?

[seryrzu]

It is in the plans yes, but probably not immediately. Would you like this to be done sooner @baozg ?

[baozg]

I also meet a install problem. Maybe singulariy or conda is more easy for people to use?