Conda

Stef Elorriaga

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Sep 24, 2024, 2:53:26 PMSep 24

to Biociphers

Is majiq in conda?

San Jewell

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Sep 24, 2024, 5:33:59 PMSep 24

to Biociphers

Hi,

Majiq uses standard python virtual environments by detault, but conda can also be used if desired. We do not have majiq in pip/conda package repositories at this time.

Thanks,

-San

On Tuesday, September 24, 2024 at 2:53:26 PM UTC-4 eel...@ncsu.edu wrote:

Is majiq in conda?

Matthew Gazzara

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Oct 10, 2024, 4:05:06 PMOct 10

to Biociphers

Hi,

If it helps, the following is how I typically set up a majiq v2 conda environment:

conda create -n majiq2 python=3.10

conda activate majiq2

cd ~/

# download htslib archive to current directory

wget https://github.com/samtools/htslib/releases/download/1.19.1/htslib-1.19.1.tar.bz2

# extract archive

tar -xf htslib-1.19.1.tar.bz2

# change into htslib source directory

cd htslib-1.19.1

# configure, make, and install htslib to ~/install/htslib-1.13

./configure --prefix=$HOME/install/htslib-1.19.1

make

make install

export HTSLIB_LIBRARY_DIR=$HOME/install/htslib-1.19.1/lib

export HTSLIB_INCLUDE_DIR=$HOME/install/htslib-1.19.1/include

pip install git+https://bitbucket.org/biociphers/majiq_academic.git

#download newly required license file and set path for the tool to work

export MAJIQ_LICENSE_FILE=/path/to/license.lic

All the best,

Matt Gazzara

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