mkweskin · February 16, 2024 18:45 · mkweskin · Feb 16, 2024
diff --git a/mamba_install.sh b/mamba_install.sh
 #!/bin/sh

 # creates a new env for a bioconda package and its dependencies. Then, it display the list
 # of newly installed binaries for the focal program.
 # The directory where the env is created is: ~/share/apps/bioinformatics/[program]/conda/[version]/

 if [ -z $1 ]; then
  echo "error: give the name of the bioconda program to be installed when calling this program"
  echo "   example: $0 augustus"
  exit 1
 fi

 # Set bioconda program name to install here:
 program=$1

 # Where your envs are located, The new env will be created in here
 install_base=~/share/apps/bioinformatics

 echo "Searching for $program in bioconda..."

 # Look up version using mamba search. This is partly to create the install path which
 # includes the version number
 mamba search bioconda::$program 2>/dev/null >/tmp/search.$$ || search_error=TRUE
 if [ ! -z $search_error ]; then
  echo "  ERROR: There was an error with finding $program in bioconda."
  rm -f /tmp/search.$$
  exit 1
 fi

 version=$(tail -n 1 /tmp/search.$$ | awk '{print $2}')
 rm -f /tmp/search.$$
 echo "  found $version."

 env_dir=$install_base/$program/conda/$version

 # exit if there's already a directory in the destination
 if [ -d $env_dir ]; then
  echo "ERROR: the destination directory already exists:"
  echo "  $env_dir"
  exit 1
 fi
 echo "Creating new env in: $env_dir"

 # Install the package into the designated directory
 # Note that the version ISN'T specified here. I want mamba to choose the version again.
 mamba create -y -q -c bioconda -c conda-forge --override-channels -p $env_dir $program 2>/dev/null || create_error=TRUE

 if [ ! -z $create_error ]; then
  echo "ERROR: There was an error when creating the environment"
  exit 1
 fi


 # List the programs that were installed for the focal program.
 # Other files in the env's bin are not included.

 # Check for the expected json file
 json="$env_dir/conda-meta/$program-$version-*.json"
 if [ ! -f $josn ]; then
  echo "ERROR: something went wrong. The file $env_dir/conda-meta/$program-$version-*.json was expected, but now found."
  echo "  The version that was expected was $version, perhaps a different version was installed?"
  exit 1
 fi


 echo "Executables now available for $program:"
 grep -E '^ *.\"bin' $env_dir/conda-meta/$program-$version-*.json | sed -r -e 's/^ *"bin\///' -e 's/\",?$//' | column -c 80

 echo "mamba activate $env_dir"

 exit 0
	#!/bin/sh

	# creates a new env for a bioconda package and its dependencies. Then, it display the list
	# of newly installed binaries for the focal program.
	# The directory where the env is created is: ~/share/apps/bioinformatics/[program]/conda/[version]/

	if [ -z $1 ]; then
	echo "error: give the name of the bioconda program to be installed when calling this program"
	echo " example: $0 augustus"
	exit 1
	fi

	# Set bioconda program name to install here:
	program=$1

	# Where your envs are located, The new env will be created in here
	install_base=~/share/apps/bioinformatics

	echo "Searching for $program in bioconda..."

	# Look up version using mamba search. This is partly to create the install path which
	# includes the version number
	mamba search bioconda::$program 2>/dev/null >/tmp/search.$$ \|\| search_error=TRUE
	if [ ! -z $search_error ]; then
	echo " ERROR: There was an error with finding $program in bioconda."
	rm -f /tmp/search.$$
	exit 1
	fi

	version=$(tail -n 1 /tmp/search.$$ \| awk '{print $2}')
	rm -f /tmp/search.$$
	echo " found $version."

	env_dir=$install_base/$program/conda/$version

	# exit if there's already a directory in the destination
	if [ -d $env_dir ]; then
	echo "ERROR: the destination directory already exists:"
	echo " $env_dir"
	exit 1
	fi
	echo "Creating new env in: $env_dir"

	# Install the package into the designated directory
	# Note that the version ISN'T specified here. I want mamba to choose the version again.
	mamba create -y -q -c bioconda -c conda-forge --override-channels -p $env_dir $program 2>/dev/null \|\| create_error=TRUE

	if [ ! -z $create_error ]; then
	echo "ERROR: There was an error when creating the environment"
	exit 1
	fi


	# List the programs that were installed for the focal program.
	# Other files in the env's bin are not included.

	# Check for the expected json file
	json="$env_dir/conda-meta/$program-$version-*.json"
	if [ ! -f $josn ]; then
	echo "ERROR: something went wrong. The file $env_dir/conda-meta/$program-$version-*.json was expected, but now found."
	echo " The version that was expected was $version, perhaps a different version was installed?"
	exit 1
	fi


	echo "Executables now available for $program:"
	grep -E '^ .\"bin' $env_dir/conda-meta/$program-$version-.json \| sed -r -e 's/^ *"bin\///' -e 's/\",?$//' \| column -c 80

	echo "mamba activate $env_dir"

	exit 0