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kircherlab / CADD-scripts

CADD scripts release for offline scoring. For more information about CADD, please visit our website
http://cadd.gs.washington.edu
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Issues installing pyrle #69

Open joreynajr opened 1 month ago

joreynajr commented 1 month ago

Hi,

I am trying to run the example but I'm running into an issue below. Seems as if snakemake tries to install some packages and the like but fails on pyrle?

  copying tests/__init__.py -> build/lib.linux-x86_64-3.6/tests
  creating build/lib.linux-x86_64-3.6/pyrle
  copying pyrle/version.py -> build/lib.linux-x86_64-3.6/pyrle
  copying pyrle/rledict.py -> build/lib.linux-x86_64-3.6/pyrle
  copying pyrle/methods.py -> build/lib.linux-x86_64-3.6/pyrle
  copying pyrle/__init__.py -> build/lib.linux-x86_64-3.6/pyrle
  copying pyrle/rle.py -> build/lib.linux-x86_64-3.6/pyrle
  creating build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/__init__.py -> build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/coverage.pyx -> build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/rle.pyx -> build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/getitem.pyx -> build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/getitem.c -> build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/rle.c -> build/lib.linux-x86_64-3.6/pyrle/src
  copying pyrle/src/coverage.c -> build/lib.linux-x86_64-3.6/pyrle/src
  running build_ext
  building 'pyrle.src.rle' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/pyrle
  creating build/temp.linux-x86_64-3.6/pyrle/src
  /mnt/BioAdHoc/Groups/vd-ay/jreyna/software/CADD-scripts-1.7/envs/conda/738489c3f99641482618d1c3a806142a_/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /mnt/BioAdHoc/Groups/vd-ay/jreyna/software/CADD-scripts-1.7/envs/conda/738489c3f99641482618d1c3a806142a_/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/BioAdHoc/Groups/vd-ay/jreyna/software/CADD-scripts-1.7/envs/conda/738489c3f99641482618d1c3a806142a_/include -fPIC -I. -I/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/CADD-scripts-1.7/envs/conda/738489c3f99641482618d1c3a806142a_/include/python3.6m -c pyrle/src/rle.c -o build/temp.linux-x86_64-3.6/pyrle/src/rle.o
  In file included from pyrle/src/rle.c:29:
  /mnt/BioAdHoc/Groups/vd-ay/jreyna/software/CADD-scripts-1.7/envs/conda/738489c3f99641482618d1c3a806142a_/include/python3.6m/Python.h:39:10: fatal error: crypt.h: No such file or directory
     39 | #include <crypt.h>
        |          ^~~~~~~~~
  compilation terminated.
  error: command '/mnt/BioAdHoc/Groups/vd-ay/jreyna/software/CADD-scripts-1.7/envs/conda/738489c3f99641482618d1c3a806142a_/bin/x86_64-conda-linux-gnu-cc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyrle
ERROR: Could not build wheels for pyrle, which is required to install pyproject.toml-based projects
failed

CondaEnvException: Pip failed

Thanks in advanced,

Joaquin

visze commented 1 month ago

Hi Joaquin,

I released a new CADD-scripts version v1.7.1. Maybe you try that one. Now it is recommended to use apptainer/singularity and all environments are packed within a container and no conda builds are needed (container is 17GB large). You also need now snakemake 8.