Closed AntonioBaeza closed 2 months ago
Will have to look into it. I'm not very familiar with Conda. Currently looking at implementing a sudo-free installation.
Thank you! A sudo-free installation will be great. If by Conda even better to make the program available to beginners, intermediate users! Best
Quick update: not quite a conda-forge/bioconda package release, but now works without sudo (see below). The Circos release in bioconda misbehaves if installed at the same time as minimap2/mashmap/diamond (due to clashes between dependencies). Works fine however if installed from its binaries once its dependencies are installed.
### Tested on Ubuntu-22.04.3 LTS (WSL2)
##########################################################################################
##### Installing Miniconda
##########################################################################################
# https://docs.anaconda.com/free/miniconda/index.html
CONDA_DIR=$HOME ## Replace by desired conda installation directory
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -P $CONDA_DIR
chmod +x $CONDA_DIR/Miniconda3-latest-Linux-x86_64.sh
$CONDA_DIR/Miniconda3-latest-Linux-x86_64.sh
## Do you wish to update your shell profile to automatically initialize conda? => yes
rm $CONDA_DIR/Miniconda3-latest-Linux-x86_64.sh
exit
## Reopen shell
## Installing the libmamba solver (faster solves)
# https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community
conda update -n base conda
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
conda config --set auto_activate_base false
##########################################################################################
##### Creating a conda environment for SYNY
##########################################################################################
INSTALL_DIR=$HOME/SYNTENY # Replace by desired installation directory
CONFIG=~/.profile # Desired configuration file
conda create --name syny
conda activate syny
conda config --add channels bioconda
conda config --add channels conda-forge
## Python / Perl dependencies
conda install --yes \
matplotlib \
pandas \
seaborn \
scipy \
libgd \
perl-perlio-gzip \
perl-getopt-argvfile \
perl-clone \
perl-config-general \
perl-font-ttf \
perl-list-moreutils \
perl-math-bezier \
perl-math-round \
perl-math-vecstat \
perl-params-validate \
perl-readonly \
perl-regexp-common \
perl-set-intspan \
perl-statistics-basic \
perl-SVG \
perl-text-format \
perl-gd
## alignment/homology tools
conda install --yes \
minimap2">=2.28" \
mashmap">=3.1.3" \
diamond">=2.1.9"
## Installing Text::Roman manually => not found in conda repositories
mkdir -p $INSTALL_DIR/PERL5
wget https://cpan.metacpan.org/authors/id/S/SY/SYP/Text-Roman-3.5.tar.gz -P $INSTALL_DIR
tar -zxvf $INSTALL_DIR/Text-Roman-3.5.tar.gz -C $INSTALL_DIR
mv $INSTALL_DIR/Text-Roman-3.5/lib/* $INSTALL_DIR/PERL5/
rm -R $INSTALL_DIR/Text-Roman-3.5*
conda env config vars set PERL5LIB=$PERL5LIB:$INSTALL_DIR/PERL5
conda activate syny
## Installing Circos (outside conda)
wget \
--no-check-certificate \
https://circos.ca/distribution/circos-0.69-9.tgz \
-P $INSTALL_DIR \
tar -zxvf $INSTALL_DIR/circos-0.69-9.tgz -C $INSTALL_DIR && rm $INSTALL_DIR/circos-0.69-9.tgz
echo "export PATH=\$PATH:$INSTALL_DIR/circos-0.69-9/bin" >> $CONFIG
## Installing Syny (outside conda)
git clone https://github.com/PombertLab/SYNY.git $INSTALL_DIR/SYNY
echo "export PATH=\$PATH:$INSTALL_DIR/SYNY" >> $CONFIG
source $CONFIG
##########################################################################################
##### Completion => should be ready to run
##########################################################################################
conda activate syny
Thank you, I will try soon! Best
Created a SYNY.yaml file to simplify things + added a section titled "Installing dependencies with Conda (does not require sudo privileges)" to the Readme.
SYNY (version 1.1a) is now available in conda (took me a while to work out the kinks). Tested the conda release in a fresh Ubuntu VM; ran without issue.
To install syny with conda:
# Creating a conda environment
conda create -n syny
# Activating the conda environment
conda activate syny
## Installing syny within the conda environment
conda install syny -c conda-forge -c bioconda
WIll mark this issue as resolved but let me know if you encounter issue(s).
Thank you!!!
Any chance to install via conda?