successfully installed majiq2.2 but not able to call majiq

[Angad Kumar]

Hi paul,

I do able to install the majiq and voila by using below command

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pip install git+https://bitbucket.org/biociphers/majiq_academic.git#egg=majiq

Collecting majiq

  Cloning https://bitbucket.org/biociphers/majiq_academic.git to /tmp/pip-install-8iq8w23n/majiq_64bbaab8737a4dcc99cc9148c7dca404

Requirement already satisfied: Click==7.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (7.0)

Requirement already satisfied: Cython==0.29.14 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (0.29.14)

Requirement already satisfied: Flask==1.0.2 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.0.2)

Requirement already satisfied: Flask-Session==0.3.1 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (0.3.1)

Requirement already satisfied: Flask-WTF==0.14.2 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (0.14.2)

Requirement already satisfied: gitdb2==2.0.6 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (2.0.6)

Requirement already satisfied: GitPython==3.0.5 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (3.0.5)

Requirement already satisfied: gunicorn==19.9.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (19.9.0)

Requirement already satisfied: h5py==2.10.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (2.10.0)

Requirement already satisfied: itsdangerous==1.1.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.1.0)

Requirement already satisfied: Jinja2==2.11.1 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (2.11.1)

Requirement already satisfied: MarkupSafe==1.1.1 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.1.1)

Requirement already satisfied: numpy==1.18.1 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.18.1)

Requirement already satisfied: psutil==5.6.7 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (5.6.7)

Requirement already satisfied: scipy==1.4.1 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.4.1)

Requirement already satisfied: six==1.14.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.14.0)

Requirement already satisfied: smmap2==2.0.5 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (2.0.5)

Requirement already satisfied: waitress==1.1.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (1.1.0)

Requirement already satisfied: Werkzeug==0.16.0 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (0.16.0)

Requirement already satisfied: WTForms==2.2.1 in /home2/s202223/tools/MajiQ/env/lib/python3.8/site-packages (from majiq) (2.2.1)

-----------------------------

After this I do able to call voila but not majiq. Could you please suggest the solution.

Thanks

Angad

[Chen]

Hi,

I'm having the same problem. 

The env/bin directory contains voila, but not majiq:

I would really appreciate a solution. 

Chen

[Melina Klostermann]

Hi Chen,

I had the same problem and this solution worked for me. The trick is to not install anything in the new python envirnoment before installing majiq. This means not to install wheel. You will get an error  `unable to build wheels for majiq`. But if you ignore that error and finish the installation you afterwards have a working majiq and voila bin. With wheels it says `sucessfully installed` but then only voila is there.

I found a comment of the developers somewhere in this forum, where they sugested this. They said they are working on making majiq work with wheels again. (the majiq 2.1 version can be installed with wheels).

I hope this helps!

pip install htslib
export HTSLIB_LIBRARY_DIR=/path/to/htslib/lib
export HTSLIB_INCLUDE_DIR=/path/to/htslib/include

on mac:
gcc (installs gcc)
export CC=/path/to/gcc/bin/gcc-version
export CXX=/path/to/gcc/bin/g++-version


python -m venv majiq2.2  # 3.6 should work, but as Paul mentioned, we prefer to support python 3.8 now
source majiq2.2/bin/activate
# no other pip steps before directly installing majiq
pip install git+https://bitbucket.org/biociphers/majiq_academic.git#egg=majiq

! Ignore error about missing wheel and git !!!

[Chen]

Hi Melina,

Thanks so much for your help and quick response! It seems to be working now.

Chen