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WGLab / LIQA

Long-read Isoform Quantification and Analysis
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Installing LIQA #37

Closed dvirdi01 closed 3 months ago

dvirdi01 commented 8 months ago

I installed liqa through pip but when I run liqa in my terminal it says Traceback (most recent call last): File "/storage/..../..../..../.../..../bin/liqa", line 5, in from liqa_src.liqa import main File "/storage/..../...../...../..../..../lib/python3.12/site-packages/liqa_src/liqa.py", line 3, in from liqa_src import my_functions as my File "/storage/..../..../..../.../..../.../python3.12/site-packages/liqa_src/my_functions.py", line 59, in import imp ModuleNotFoundError: No module named 'imp'

sparthib commented 7 months ago

Hi @dvirdi01, I ran into the same error. Were you able to solve this issue? Thanks!

I'm pasting my environment information here for more context: @huyustats, if you have any insights please let me know, thanks! 

name: LIQA
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - binutils_impl_linux-64=2.40=hf600244_0
  - bwidget=1.9.14=ha770c72_1
  - bzip2=1.0.8=hd590300_5
  - c-ares=1.22.1=hd590300_0
  - ca-certificates=2023.11.17=hbcca054_0
  - cairo=1.18.0=h3faef2a_0
  - curl=8.4.0=hca28451_0
  - expat=2.5.0=hcb278e6_1
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=h77eed37_1
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - freetype=2.12.1=h267a509_2
  - fribidi=1.0.10=h36c2ea0_0
  - gcc_impl_linux-64=13.2.0=h338b0a0_3
  - gettext=0.21.1=h27087fc_0
  - gfortran_impl_linux-64=13.2.0=h76e1118_3
  - graphite2=1.3.13=h58526e2_1001
  - gxx_impl_linux-64=13.2.0=h338b0a0_3
  - harfbuzz=8.3.0=h3d44ed6_0
  - icu=73.2=h59595ed_0
  - kernel-headers_linux-64=2.6.32=he073ed8_16
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.21.2=h659d440_0
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libblas=3.9.0=20_linux64_openblas
  - libcurl=8.4.0=hca28451_0
  - libdeflate=1.19=hd590300_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-devel_linux-64=13.2.0=ha9c7c90_103
  - libgcc-ng=13.2.0=h807b86a_3
  - libgfortran-ng=13.2.0=h69a702a_3
  - libgfortran5=13.2.0=ha4646dd_3
  - libglib=2.78.1=h783c2da_1
  - libgomp=13.2.0=h807b86a_3
  - libiconv=1.17=h166bdaf_0
  - libjpeg-turbo=3.0.0=hd590300_1
  - liblapack=3.9.0=20_linux64_openblas
  - libnghttp2=1.58.0=h47da74e_0
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.25=pthreads_h413a1c8_0
  - libpng=1.6.39=h753d276_0
  - libsanitizer=13.2.0=h7e041cc_3
  - libsqlite=3.44.2=h2797004_0
  - libssh2=1.11.0=h0841786_0
  - libstdcxx-devel_linux-64=13.2.0=ha9c7c90_103
  - libstdcxx-ng=13.2.0=h7e041cc_3
  - libtiff=4.6.0=ha9c0a0a_2
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp-base=1.3.2=hd590300_0
  - libxcb=1.15=h0b41bf4_0
  - libzlib=1.2.13=hd590300_5
  - make=4.3=hd18ef5c_1
  - ncurses=6.4=h59595ed_2
  - openssl=3.2.0=hd590300_1
  - pango=1.50.14=ha41ecd1_2
  - pcre2=10.42=hcad00b1_0
  - pip=23.3.1=pyhd8ed1ab_0
  - pixman=0.42.2=h59595ed_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - python=3.12.0=hab00c5b_0_cpython
  - r-base=4.3.2=hb8ee39d_1
  - readline=8.2=h8228510_1
  - sed=4.8=he412f7d_0
  - setuptools=68.2.2=pyhd8ed1ab_0
  - sysroot_linux-64=2.12=he073ed8_16
  - tk=8.6.13=noxft_h4845f30_101
  - tktable=2.10=h0c5db8f_5
  - wheel=0.42.0=pyhd8ed1ab_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.1.1=hd590300_0
  - xorg-libsm=1.2.4=h7391055_0
  - xorg-libx11=1.8.7=h8ee46fc_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-libxt=1.3.0=hd590300_1
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.5.5=hfc55251_0
  - pip:
      - astor==0.8.1
      - autograd==1.6.2
      - autograd-gamma==0.5.0
      - contourpy==1.2.0
      - cycler==0.12.1
      - fonttools==4.45.1
      - formulaic==0.6.6
      - future==0.18.3
      - interface-meta==1.3.0
      - kiwisolver==1.4.5
      - lifelines==0.27.8
      - liqa==1.3.4
      - matplotlib==3.8.2
      - numpy==1.26.2
      - packaging==23.2
      - pandas==2.1.3
      - pillow==10.1.0
      - pyparsing==3.1.1
      - pysam==0.22.0
      - python-dateutil==2.8.2
      - pytz==2023.3.post1
      - scipy==1.11.4
      - six==1.16.0
      - typing-extensions==4.8.0
      - tzdata==2023.3
      - wrapt==1.16.0
prefix: /users/sparthib/.conda/envs/LIQA
agouru55 commented 3 months ago

Yes, the above comment has the correct packages. Perhaps try to install with git clone instead (as it will have the most up to date version) and see if you still run into issues. More info is on the Install link: https://github.com/WGLab/LIQA/blob/master/doc/Install.md