SaundersLab / marple

Pipeline for analysis of stem rust (Pgt) and yellow rust (Pst) reads for MARPLE
https://marple-diagnostics.org/
GNU General Public License v3.0
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Issue with updating softwares #19

Closed 502107 closed 1 month ago

502107 commented 3 months ago

Potential bug when updating softwares/mamba environment, where the initialisation script for mamba and conda in .bashrc gets removed, so mamba is not recognised in the system. Only need to add the script (below) in the .bashrc -- will update the installation script once I get the chance to replicate the issue:

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
export MAMBA_EXE='/home/marple/marple/bin/micromamba';
export MAMBA_ROOT_PREFIX='/home/marple/micromamba';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/marple/micromamba/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/marple/micromamba/etc/profile.d/conda.sh" ]; then
        . "/home/marple/micromamba/etc/profile.d/conda.sh"
    else
        export PATH="/home/marple/micromamba/bin:$PATH"
    fi
fi
unset __conda_setup

if [ -f "/home/marple/micromamba/etc/profile.d/mamba.sh" ]; then
    . "/home/marple/micromamba/etc/profile.d/mamba.sh"
fi
# <<< conda initialize <<<